Sequence
atgc intronic sequence ATGC exonic sequence...gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaataaatattaatccacatttcaataacaacatttctgacctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
Basic information
species | Glycine max |
transcript | GLYMA10G08610.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G08610.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os12g05900.1 (Oryza sativa), 3'ss of exon 4
gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaataaatattaatccacatttcaataacaacatttctgacctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
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------------------gtagtgtgttatcctattgcgatcatggtactga-tatt--tcattaggtggattctaactgttgtcacacatgtaatgcagATGGCAGATCCCTTGACTGCATTGATGTATGCAGTACAAGTGATGAATTTTCTTAAGATGCTAATACAAAAAACCCTCAAGGATAGAGAAGAGTCTGATC
upper sequence: GLYMA10G08610.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os11g05540.1 (Oryza sativa), 3'ss of exon 4
gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaataaatattaatccacatt-tcaataacaacatttctg-acctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
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-----------------------gtaatgcactgtcctaa--taataaacttatgattttaagtgtggtcgatgcttactgtcatgcacatatgtaatgcagATGTCAGATCCATTGACCGCACTGATGTATGCGGTGCAAGTGATGAATTTTCTCAAGATGCTAATACAGAAGACCCTCAAGGGTAGACAAGAGTCCAATC
upper sequence: GLYMA10G08610.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G136069_T01 (Zea mays), 3'ss of exon 3
gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaat--------aaatattaatccacatttcaataacaacatttctgacctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
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gtattgcattgtgctaatattgtagcaattagcaaactagcaatatatacctcaccccgagcagtggaacggttatgcgtgctaactattagcaaacttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCCACTC
upper sequence: GLYMA10G08610.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G113073_T01 (Zea mays), 3'ss of exon 4
gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaataaatattaatccacatttcaataacaacatttctgacctgtatac--tacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
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gtattgcattgtgctgatacgata---gcgattagc---aaactatcaatatatacttcacc-catcacaatgatgctaactatagcacgcttacaatgcagATGGCAGATCCTTTGACTGCACTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGATGCTGGTACAAAAGACCCTCAAGGATAGAGAGGAGTCGACCC
upper sequence: GLYMA10G08610.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g03140.t01 (Vitis vinifera), 3'ss of exon 4
-----gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaataaatattaatccacatttca-ataacaacatttctgacctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
| || | | | | || | | || | || ||| | || || | || | | || | || | |||| | |||||||||||||| ||||| || |||||| ||| ||| ||||||||||||||||||||||| | || | ||| || || ||||| |||| || | |
atcctcttttaaataaactcactgatgtttttcttattttgatatagtttt--gtacattctggtcaatgtgaggtgcaatgatatctt----ctgttggttgcagATGGCAGATCCCTTGACAGCCTTGATGTATGCAGTCCAAGTGATGAATTTTCTCAAGACTTTGATAATCAGGACGCTTAGGGAAAGGGAGGACTCAATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaataaatattaatccacatttcaataacaacatttctgacctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
ttctgac putative branch site (score: 2)
aaatattaat TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttgcaagactatagtatagtatgtggtactggtctaaggttatcaataaatattaatccacatttcaataacaacatttctgacctgtatactacagATGGCAGATCCTTTGACGGCTTTGATGCATGTAGTACAAGTGATGAATTTTCTCAAGACCCTTGAGATGAAGACACTAAGAGAAAGAGAGGGGTCTACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - tgcaaga
- - - - - - - - - - -gtatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - atccaca