Sequence
atgc intronic sequence ATGC exonic sequence...gtctaattgtggagctaatccatgggttcagtttgggtcataatgttaacaggatcagtcatattaacatatctgtatgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
Basic information
species | Glycine max |
transcript | GLYMA05G30630.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os08g03440.1 (Oryza sativa), 3'ss of exon 6
-gtctaattgtggagctaatccatgggttcagtttgg-gtcataatgttaacaggatcagtcatat-taacatatctgtatgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
| | |||| | | | | || | | || | || | || | | || ||| || || ||| ||| ||||||| ||||| |||| ||||| || ||||| |||| ||| | || | |||| || | || |||| ||||||||||||||||||||||||
cattttattgacatttggactcttcaccttgaaatgacattaaaaggagaaaaacatgaatttgatgtaatttac---taaccttctactagcgcaaatgcagATCTTCTTCCATCCCGAGATTTACTCTGCCGACTTCTCCACTCCTCTACCTGAACTAATTGATAGCTGTGTTCAATCTGCGCCAATTGACACAAGGAGAG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 5
lower sequence: AC205703.4_FGT002 (Zea mays), 3'ss of exon 6
gtctaattgtggagctaatccatgggttcagtttgggtcataatgttaacaggatcagt-catattaacatatctgtatgctttccctat--gatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
| ||| | | || || || || ||| | | ||||||| | || | || |||| | | | | | | | | || | |||||| ||||| || || ||||||||| || ||||| ||||| ||||||| |||||| || ||||||||||| || || | ||||| |||||||||||
-tgcaatgct--aacttttcttcaagtacatttttgctatacatgttaattttagcattatattttaattcaaccttcttatattagtgtcaaatctgcgcagATCTTCTTCAACCCAGAGATATATAACAACGACTTCACCACTCCTTTGCAAGTTGTTATTGACAAGTGCATCCAATCATCTCCAATCGACACAAGGAGGG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G305332_T01 (Zea mays), 3'ss of exon 1
-gtctaattgtggagctaatccatgggttcagtttgggtcataatgttaacaggatcagtcata--ttaacatatctgtatgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
| | | | | | | || ||||||| |||||| || || ||||| | || | | | | | | | ||||||| ||||| ||||||||||| || ||||| |||| ||||| || | | || || || || |||||||||| ||||||||||||||||||
tttgttagaataaacttttaacttgttttcagtt--ggtcatgattttttttaaga-agtcagaatttggtgtgcgtctctaatcatctagcaacaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGACTTCTCCACTCCTTTACCTGAGTTGATTGATAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G136662_T01 (Zea mays), 3'ss of exon 5
-gtctaattgtggagctaatccatgggttca-gtttgggtcataatgttaacaggatcagtcatattaacatatctgtatgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
|| | ||| || | ||| | || | | | ||||| | |||| || |||| || | || | | | ||||||| ||||| ||||||||||| || || || |||| |||||||| | | || ||||| || |||||||||| ||||||||||||||||||
taacttgcttgggactaaaagactatgttgatgtacagttggtcatgttttttaggtcagaattaggtgtgcatctctaatcatttacca--acaaatgcagATCTTCTTCAATCCTGAGATTTACTCTGCCGATTTCTCCACTCCTTTGCCCGAGTTGATTGACAACTGTGTTCAGTCTGCACCAATTGACACAAGGAGAG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G13180.1 (Arabidopsis thaliana), 3'ss of exon 5
gtctaattgtggagctaatccatgggtt-cagtttgggtcataatgttaacaggatcagtcatattaacat--atctgta-tgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
|| | | | || ||| | ||| | || | | | | | || | || | || ||| || | | || | | ||| | ||||||||||| |||||||| ||| |||||| || || |||| |||| ||| |||||||| || ||||||||||| |||||||||||| | |||
---caagagagtaactggaaagtggaacataatttcctttattgttcttgc-gtttttgttctgctattaccgatgagtaatgttgagattttgtgtgttacagGTGTTCTTTAATCCAGAGATATACAGCAATGACTTCACAACTACTTTACCAGCTGTGATAGACAAATGTATTCAGTCTGCACCAATTGACACACGAAGAG
upper sequence: GLYMA05G30630.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0137g00280.t01 (Vitis vinifera), 3'ss of exon 5
-gtctaattgtggagctaatccatgggttcagtttgggtcataatgttaacaggatcagtcatattaacatatctgt-atgctttcccta-tgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
|| || ||||| | || | | | | || ||| | | | | || | | | | ||| || || || ||||||||||||| ||||||||||| || |||| || ||| | |||||||| |||| ||||||||||||||| ||||||||||| |||||||||||||| ||
tgtttacttgtgcattgcatttc---atctactagatgatgctttgataagtcttttaaaaaaaggaatttgtttttgatgattaatctggctgattatgcagATTTTCTTCAATCCTGAGATCTACAGCAGCGATTTTGCAACCCCTTTACCAGCTGTAATAGACAAGTGTATTCAGTCTGCACCAATTGACACAAGAAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaacaggatcagtcatattaacatatctgtatgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
tattaac putative branch site (score: 1)
tttctgc putative PPT
tcatattaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctaattgtggagctaatccatgggttcagtttgggtcataatgttaacaggatcagtcatattaacatatctgtatgctttccctatgatttctgcagATTTTCTTTAATCCTGAGATATATGGCAGTGACTTTACCACCCCTTTGCCAGTTGTAATAGACAAGTGCATTCAGTCTGCGCCAATTGACACAAGGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - -tgtggag
- - - - - - - - - tccatgg
- - - - - - - - - - - - - - - gtttggg