Sequence
atgc intronic sequence ATGC exonic sequencegtattagttttcatggcattcctattttatacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
Basic information
species | Glycine max |
transcript | GLYMA06G08710.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
gtattagttttcatggcattcctattttatacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattg-tagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
|| | || ||| || | || ||| ||||| | ||| |||||| || ||||||||||| ||||| | |||||||||| | ||||| ||||| |||||||||||||||||||| || | | ||||||||||| || ||||||| |||||
----------gtctgctaacactgtttgatgtcc--ttccatgctgaaagattaagatattg-atttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
upper sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
--gtattagttttcatggcattcctatttta-tacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
| || | ||| | || | | | | ||| | | | |||| | ||||| | | ||| || ||||| | |||||| ||||||| |||| | | | |||||||| ||||||||||| || || || ||| | ||||||||||||||||| |||||||| |
gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaatatgatgg-catatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
upper sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 3
------gtattagttttcatggcattcctattttatacctgatttcatcatgaaaagtatg---tttatcatatttatcacacaaa-ttgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
||| ||||| | | | | ||| || | | || | | |||| | || || | || |||||||||| ||||| | ||||||||| | | ||| ||||| ||||||||||||| |||||| ||| | | |||||||||||||| || || |||||||
gtatgtatataagtttaaaccttaaaagttaaaattgtctggtta-gttgtaaactctttaaattttaacgccttattcttttgagcttttagCCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAAGAAGTTTTTGGCGGGGTACGTGCAAGATATCCACAATACTACGCAGCAT
upper sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------------------------------gtattagttttcatggcattcctattttat------acctgatttcatcatgaaaagtatgtttatcatatt-tatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
| | |||| |||| | | | | | ||| ||| | || |||| |||| || || | | || | |||||||||| || || |||| |||||||||||| ||||| ||||| |||||||||||||||||||| || | | ||||||||||| |||||||| |||||||
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
upper sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
gtattagttttcatggcattcct-attttatacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
|||| | | ||| | ||| | |||| |||||| ||| | | || ||| | | | ||||| |||| |||||| ||||| | ||||||||| | | || ||||||||||||||||||| |||||| || || | |||||||||||||| |||||||||||||
gtatgtgcatacattttaaaccttaattta---ctgatt--gtcaatagcaa-atccttaatgcttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
upper sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
--gtattagttttcatggcattcctattttatacctgatttcatcatgaaaagtatgtttatcat---atttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
| || ||||||| | | || || ||| | ||||| | | |||| || ||| || || || ||||| | ||| | |||||| ||||| | || |||||||| ||||||||||| ||||| || ||| | |||||||||||||| || ||||||||||
gttcaatatgtttcatgcttgcaaaactctacttcttattcta--atgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
upper sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G08790.1 (Arabidopsis thaliana), 3'ss of exon 3
--------gtattagttttcatggcattcctattttatacc--tgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
| || |||| | | | || | |||| | | ||| | ||| | || ||||||| || | || || |||||| | ||| || | |||||||||||||| |||||||||||||||||||| ||| ||| ||| | |||| ||||||| ||||| |||||||
gtcaggctatgtttcttttaaacgattgtttaatctataacaatagttttgt-gtgacaccta-acttatcatgttgtttgttaaacttatagCCTAACATCCAAGTGAAGGAGAAGATATTGATACTTATAGATACTTGGCAAGAGAGCTTTTCAGGTCCACAAGGAAGACATCCACAATATTACGCAGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
acctgat putative branch site (score: 4)
aaaagtatgtttatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattagttttcatggcattcctattttatacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA