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5 months ago
ManuelDB
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110
NCBI has a useful tool that collect the information of all transcripts ID versions and allows you to see differences. Here one example
https://www.ncbi.nlm.nih.gov/nuccore/NM_002734?report=girevhist
I am interested to see if there are differences in the sequence between transcript versions. The website provides a BLAST analysis such as the one I provided below.
In the sequence comparison, I can see that sometimes the base in the subject is capital while in the opposite is lowercase. This is not considered a mismatch by BLAST.
My question is what does this mean???
I show an example here
Query 61 AGCTCGGTAcgccgccgcctcgcacccgcagcctcgcgcccgccgccgcccgTCCCCAGA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 112 AGCTCGGTACGCCGCCGCCTCGCACCCGCAGCCTCGCGCCCGCCGCCGCCCGTCCCCAGA 171
and the almost complete BLAST result here:
Accession Gi Update Date
NM_002734.5 1779521771 Mar 21, 2024 08:35 PM
NM_002734.4 443497962 Sep 25, 2019 01:48 AM
BLASTN 2.15.0+
Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.
Database: User specified sequence set (Input: /dev/shm/girevhist_2QCl0WI).
1 sequences; 4,325 total letters
Query= NM_002734.5 Homo sapiens protein kinase cAMP-dependent type I
regulatory subunit alpha (PRKAR1A), transcript variant 1, mRNA
Length=4253
Score E
Sequences producing significant alignments: (Bits) Value
NM_002734.4 Homo sapiens protein kinase cAMP-dependent type I reg... 7854 0.0
>NM_002734.4 Homo sapiens protein kinase cAMP-dependent type I regulatory
subunit alpha (PRKAR1A), transcript variant 1, mRNA
Length=4325
Score = 7854 bits (4253), Expect = 0.0
Identities = 4253/4253 (100%), Gaps = 0/4253 (0%)
Strand=Plus/Plus
Query 1 GGAGCTGTCGCCTAGCCGCTATCGCAGAGTGGAGCGGGGCTGGGAGCAAAGCGCTGAGGG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 52 GGAGCTGTCGCCTAGCCGCTATCGCAGAGTGGAGCGGGGCTGGGAGCAAAGCGCTGAGGG 111
Query 61 AGCTCGGTAcgccgccgcctcgcacccgcagcctcgcgcccgccgccgcccgTCCCCAGA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 112 AGCTCGGTACGCCGCCGCCTCGCACCCGCAGCCTCGCGCCCGCCGCCGCCCGTCCCCAGA 171
Query 121 GAACCATGGAGTCTGGCAGTACCGCCGCCAGTGAGGAGGCACGCAGCCTTCGAGAATGTG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 172 GAACCATGGAGTCTGGCAGTACCGCCGCCAGTGAGGAGGCACGCAGCCTTCGAGAATGTG 231
Query 181 AGCTCTACGTCCAGAAGCATAACATTCAAGCGCTGCTCAAAGATTCTATTGTGCAGTTGT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 232 AGCTCTACGTCCAGAAGCATAACATTCAAGCGCTGCTCAAAGATTCTATTGTGCAGTTGT 291
Query 241 GCACTGCTCGACCTGAGAGACCCATGGCATTCCTCAGGGAATACTTTGAGAGGTTGGAGA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 292 GCACTGCTCGACCTGAGAGACCCATGGCATTCCTCAGGGAATACTTTGAGAGGTTGGAGA 351
Query 301 AGGAGGAGGCAAAACAGATTCAGAATCTGCAGAAAGCAGGCACTCGTACAGACTCAAGGG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 352 AGGAGGAGGCAAAACAGATTCAGAATCTGCAGAAAGCAGGCACTCGTACAGACTCAAGGG 411
Query 361 AGGATGAGATTTCTCCTCCTCCACCCAACCCAGTGGTTAAAGGTAGGAGGCGACGAGGTG 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 412 AGGATGAGATTTCTCCTCCTCCACCCAACCCAGTGGTTAAAGGTAGGAGGCGACGAGGTG 471
Query 421 CTATCAGCGCTGAGGTCTACACGGAGGAAGATGCGGCATCCTATGTTAGAAAGGTTATAC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 472 CTATCAGCGCTGAGGTCTACACGGAGGAAGATGCGGCATCCTATGTTAGAAAGGTTATAC 531
Query 481 CAAAAGATTACAAGACAATGGCCGCTTTAGCCAAAGCCATTGAAAAGAATGTGCTGTTTT 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 532 CAAAAGATTACAAGACAATGGCCGCTTTAGCCAAAGCCATTGAAAAGAATGTGCTGTTTT 591
Query 541 CACATCTTGATGATAATGAGAGAAGTGATATTTTTGATGCCATGTTTTCGGTCTCCTTTA 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 592 CACATCTTGATGATAATGAGAGAAGTGATATTTTTGATGCCATGTTTTCGGTCTCCTTTA 651
Query 601 TCGCAGGAGAGACTGTGATTCAGCAAGGTGATGAAGGGGATAACTTCTATGTGATTGATC 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 652 TCGCAGGAGAGACTGTGATTCAGCAAGGTGATGAAGGGGATAACTTCTATGTGATTGATC 711
Query 661 AAGGAGAGACGGATGTCTATGTTAACAATGAATGGGCAACCAGTGTTGGGGAAGGAGGGA 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 712 AAGGAGAGACGGATGTCTATGTTAACAATGAATGGGCAACCAGTGTTGGGGAAGGAGGGA 771
Query 721 GCTTTGGAGAACTTGCTTTGATTTATGGAACACCGAGAGCAGCCACTGTCAAAGCAAAGA 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 772 GCTTTGGAGAACTTGCTTTGATTTATGGAACACCGAGAGCAGCCACTGTCAAAGCAAAGA 831
Query 781 CAAATGTGAAATTGTGGGGCATCGACCGAGACAGCTATAGAAGAATCCTCATGGGAAGCA 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 832 CAAATGTGAAATTGTGGGGCATCGACCGAGACAGCTATAGAAGAATCCTCATGGGAAGCA 891
Query 841 CACTGAGAAAGCGGAAGATGTATGAGGAATTCCTTAGTAAAGTCTCTATTTTAGAGTCTC 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 892 CACTGAGAAAGCGGAAGATGTATGAGGAATTCCTTAGTAAAGTCTCTATTTTAGAGTCTC 951
Query 901 TGGACAAGTGGGAACGTCTTACGGTAGCTGATGCATTGGAACCAGTGCAGTTTGAAGATG 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 952 TGGACAAGTGGGAACGTCTTACGGTAGCTGATGCATTGGAACCAGTGCAGTTTGAAGATG 1011
Query 961 GGCAGAAGATTGTGGTGCAGGGAGAACCAGGGGATGAGTTCTTCATTATTTTAGAGGGGT 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1012 GGCAGAAGATTGTGGTGCAGGGAGAACCAGGGGATGAGTTCTTCATTATTTTAGAGGGGT 1071
Query 1021 CAGCTGCTGTGCTACAACGTCGGTCAGAAAATGAAGAGTTTGTTGAAGTGGGAAGATTGG 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1072 CAGCTGCTGTGCTACAACGTCGGTCAGAAAATGAAGAGTTTGTTGAAGTGGGAAGATTGG 1131
Query 1081 GGCCTTCTGATTATTTTGGTGAAATTGCACTACTGATGAATCGTCCTCGTGCTGCCACAG 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1132 GGCCTTCTGATTATTTTGGTGAAATTGCACTACTGATGAATCGTCCTCGTGCTGCCACAG 1191
Query 1141 TTGTTGCTCGTGGCCCCTTGAAGTGCGTTAAGCTGGACCGACCTAGATTTGAACGTGTTC 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1192 TTGTTGCTCGTGGCCCCTTGAAGTGCGTTAAGCTGGACCGACCTAGATTTGAACGTGTTC 1251
Query 1201 TTGGCCCATGCTCAGACATCCTCAAACGAAACATCCAGCAGTACAACAGTTTTGTGTCAC 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1252 TTGGCCCATGCTCAGACATCCTCAAACGAAACATCCAGCAGTACAACAGTTTTGTGTCAC 1311
