Sequence
atgc intronic sequence ATGC exonic sequence...acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtacttgagttattaactagcagtttccacttgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
Basic information
species | Glycine max |
transcript | GLYMA04G11550.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os10g21910.1 (Oryza sativa), 3'ss of exon 13
acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtacttgagttattaact-agcagtttccacttgtta------cagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
| ||| | | ||| | ||| | | | || ||||| | || |||| | | || | | || | | ||| | |||||||||||||||||||||||||| ||||| ||| |||||| ||||| || |||||||| || |||| || || ||||| | |||
--gtaaatatatatcactataaacttttttatagaaagatgatatgctagtattatatttt-tagttgaaaaaggatctgatccgtctgtaactgtaaattcttcagTTGGATGGAAACAGTCATGTAATTTATGCGGAGACAGAAGCTGCTGGTACACGCCTTCTCATCAATGGGAGAACATGCTTATTACAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G377341_T01 (Zea mays), 3'ss of exon 14
acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtacttgagttattaactagcagtttccacttgtta--cagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
| | | || | | | ||| || ||||| | | | | | ||| || | || | | || | || |||||||||||||||||||||||||| ||||||||| ||| || ||||| || |||||||| || |||| || || ||||| || |||
gctct-tcttagtgcaatgcccacag-gctgttttaccctcgtaggtcaactttttttctattaaaaaattttctgatacatctttgtcgtaaattcttcagTTGGATGGAAACAGTCATGTAATTTATGCAGAGACAGAGGCTGCTGGTACACGCCTTCTCATTAATGGTAGAACATGCTTACTACAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 17
acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtacttgagttattaactagcagtttccacttgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
|| | | | | ||| | || | | || ||| ||| |||| || || | | | | | || | | | ||||||||||||||||| |||||||| |||||||| |||||||| | ||| || || |||| || ||||||| ||| || || | |||
-------------gtaactagttcttttttatgcttta-ttattaattagttggataaatggt--ttcgatttctgattgttaaactgcaatggctccagTTGGATGGAAACAGCCATGTAATTTATGCAGAAGAAGAAGCTGGTGGTACACGGCTTCAGATTGATGGAAAGACATGTTTATTGCAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
lower sequence: AC197672.3_FGT002 (Zea mays), 3'ss of exon 17
acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtacttgagttattaactagcagtttccacttgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
| | |||||| | ||| | | | |||| || ||| || | | || | | | | | | | | | || | | ||||||||||||||||| ||||| || |||||||| |||||||| | || || || |||| || |||||| ||| |||||| | |||
gtaacttattattttttttata-ctttattattaattagttggataaatggttttgatttcatgatgg---ttctgattgttgaactgcaatgactccagTTGGATGGAAACAGCCATGTGATTTATGCAGAAGAAGAAGCTGGCGGTACACGGCTTCAGATTAATGGAAAGACATGCTTGTTGCAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G36160.1 (Arabidopsis thaliana), 3'ss of exon 16
---acacagtggtattttatcgata--acatcactattttataactg-gtcttttgttctata---tctggtacttgagttattaactagcagtttccact--tgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
| | ||| || ||| ||| || | ||| || ||| | | ||||| | | | |||| |||| || ||||||||||| || || ||||| |||||||||||||||||||| || |||||||| ||||| || |||||||| ||||| ||||| |||
gcaagttttctgcctttgttctatattacaagacaaggacatacatgtgtcgcgcagaaaaaaacttctggagaatctcacttccttttcttgttttcactgtcattgcagTTGGATGGCAAAAGCCATGTGATATATGCAGAGGAAGAAGCTGCAGGAACTCGTCTTCTCATTGATGGAAGAACTTGTTTGCTACAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 16
-------acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtacttgagttattaactagcagtttc----cact--tgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
| | |||| ||| | ||| || ||| | || | || || || || || | ||| || ||| |||| || ||||||||||| || || ||||| ||||||||| |||||||||| | ||||| || ||||| || || ||||| |||||||| || |||
gcaagttttataactttattctat--actacaagacagagacata-catgtgtcatgcatagtaacttccttttaagaagctcacttccatttttggttcactgtcattgcagTTGGATGGTAAAAGCCATGTGATATATGCAAAGGAAGAAGCGACAGGAACCCGTCTTCTCATTGACGGAAGAACTTGCTTACTACAG
upper sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 17
-acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtactt--gagttattaactagcagtttccacttgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
| || | | | | | | | | | || | |||| || | | | |||| || || || | |||||| ||| | ||||||||||||||||||||| | || ||||| ||||||||||||||||||||||||||||| || | ||||||||||||||||||||||
tatctaggaggttgactttggtgggaattatgatcca-aagtagtctctt-ctgtttggtcaacacttccgaattgttt-ttgatagtttcagtttgctgcagTTGGATGGAAACAGTCATATTATCTATGCCGAGGAAGAAGCAGCTGGAACTCGCCTTCTCATTGGTGGAAGGACTTGCTTGCTTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttctatatctggtacttgagttattaactagcagtttccacttgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
tattaac putative branch site (score: 1)
tttccactt putative PPT
ttattaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acacagtggtattttatcgataacatcactattttataactggtcttttgttctatatctggtacttgagttattaactagcagtttccacttgttacagTTGGATGGAAACAGTCATGTAATATATGCAGAGGAAGAAGCAGCTGGAACTCGCCTTCTAATAGATGGAAGGACTTGCTTGCTTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - acatcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctggtac