Sequence
atgc intronic sequence ATGC exonic sequencegtattgatatttcttggatgttttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
Basic information
species | Glycine max |
transcript | GLYMA04G08600.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g22650.1 (Oryza sativa), 3'ss of exon 3
gtattgatatttcttggatgttttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattg-tagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
|| | | || | || ||| || | || ||| ||||| || ||| |||||| || ||||||||||||||||| | |||||||||| | ||||| ||||| |||||||||||||||||||| || || | ||||||||||| || ||||||| |||||
-------------------gtctgc-taaca---ctgtttgatgtcc--ttccatgctgaaagattaagatattg-atttattgttttgttttctagCCTGATTATCATGTAAAAGAGAAGATACTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTTCCCGTGCAAGATATCCGCAATATTATGTAGCAT
upper sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g17350.2 (Oryza sativa), 3'ss of exon 3
gtattgatatttcttggatgttttcatagccttcctattttatacctgatt-tcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
|||| |||| || | || | || || ||| | | | || | | | |||| | | |||| | | || |||||||||| |||||| | ||||||||| | | ||| ||||| ||||||||||||| |||||| ||| | | |||||||||||||| || || |||||||
gtatgtatataagtttaa-accttaaaag--ttaaaattgtctggttagttgtaaactctttaaattttaacgccttattcttttg--agcttttagCCTGATTTTCATGTGAAAGAGAAGATCCTCACTCTGATAGACACTTGGCAAGAAGTTTTTGGCGGGGTACGTGCAAGATATCCACAATACTACGCAGCAT
upper sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
gtattgatatttcttggatgt-tttcatagccttcctatttta-tacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
|| ||| | | ||||| || | | | | ||| | | |||||| | ||||| | | ||| || ||||| | |||||| ||||||| |||| | | | |||||||| ||||||||||| || || || || | ||||||||||||||||| |||||||| |
------------gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaatatgatgg-catatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
upper sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G077844_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------gtattgatatttcttggatgttttcatagccttcctattttat---------------acctgatttcatcatgaaaaatatgtttatcatatt-tatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
| || |||||| ||| | | ||| | || | ||| ||| | || |||| |||| || || | | || | |||||||||| ||||| |||| |||||||||||| ||||| ||||| |||||||||||||||||||| || | | ||||||||||| |||||||| |||||||
gtgcaaatgccttttaatattctcctttatcattattacttgccacttcgacatgggcatgcatatttgaatcatgggcaaacaaatttcttggcttgtgtttatgagtaagtaaccctattcagtaataaaaataatgtctaatctactatttcgtttgatctgtagCCTGACTATCACGTCAAAGAGAAGATATTAATTCTGATAGACACTTGGCAAGAAGCTTTTGGTGGTGCCCGTGCAAGATATCCCCAGTATTACGCAGCAT
upper sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G053925_T01 (Zea mays), 3'ss of exon 3
gtattgatatttcttggatgttttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
| | | |||| || | ||| | ||| | || || ||| | | | | ||||| |||| |||||||||||| | ||||||||| | | || ||||||||||||||||||| |||||| || || | |||||||||||||| |||||||||||||
-----------------gtatgtgcatacattttaaaccttaatttactgattgtcaatagcaa-atccttaatgcttctcttttgaaaattttagCATGATTATCATGTTAAAGAGAAGATTCTCACGCTGATAGATACTTGGCAAGAAGTTTTTGGTGGTGCACGTGCAAGATATCCACAATATTATGCAGCAT
upper sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
gtattgatatttcttggatgt-tttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcat---atttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
|| || | |||||| | | || || ||| | ||||| | |||| || ||| || || || ||||| || ||| | |||||| ||||| | || |||||||| ||||||||||| ||||| || || | |||||||||||||| || ||||||||||
------------gttcaatatgtttcatgcttgcaaaactctacttcttattcta--atgaactgctggcttatgatggtgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT
upper sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G08790.1 (Arabidopsis thaliana), 3'ss of exon 3
gtattgatatttcttggatgttttcatagccttcctattttatacc--tgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
| | || | |||| | | | || | |||| | | ||| | ||| | || ||||||| || | || || |||||| | || || | |||||||||||||| |||||||||||||||||||| ||| ||| || | |||| ||||||| ||||| |||||||
-----gtcaggctatgtttcttttaaacgattgtttaatctataacaatagttttgt-gtgacaccta-acttatcatgttgtttgttaaacttatagCCTAACATCCAAGTGAAGGAGAAGATATTGATACTTATAGATACTTGGCAAGAGAGCTTTTCAGGTCCACAAGGAAGACATCCACAATATTACGCAGCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
acctgat putative branch site (score: 4)
atttcatcatgaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgatatttcttggatgttttcatagccttcctattttatacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA