Sequence
atgc intronic sequence ATGC exonic sequence...aaacattaatattgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttgataatttcttataaaattcttgatctttctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
Basic information
species | Glycine max |
transcript | GLYMA08G24290.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g04490.1 (Oryza sativa), 3'ss of exon 12
------------------------------------------------aaacattaatattgtttccttactttactgctttcaaatatt------tatctgttaggttccttatgtttgataatttctt-ataaaattcttgatctttc---tccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
|| | | | || | || || | | || ||| |||| ||| | | | ||| |||| | | |||||| | | | |||||||| |||||||||| ||||||||||||||||| |||||||||||||||||| || | |||| | |||||||| | ||||||||||| || ||||
gtaggattgtacagtggtttgcgtgctccttattttgatagatcacatggctgctagcactctacccctctttccctttctatcatccttgctcagtatttgtttttttcactttactggatggcatctttaccatgaacttgatttgttatgtgcagCTTGGGGAAACCATTTATCCAATGAAGGAAGATTTCATTATGGTTCATTTGCAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAAACGTT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G470556_T01 (Zea mays), 3'ss of exon 11
----------------------------------------aaacattaatat-tgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttga--taatttcttataaaattcttgatctttc--tccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
| || ||| | | | | | ||| || | | | | | | | ||| | | | | ||| ||||| || | ||| | | | | | ||||||||||||||||| | || |||||||||||||| |||||||| ||||||||| || |||||| | ||| |||| | ||||||||||| | ||||
gtaagcttctttgatttctgtgtacttcctgctctcataaatactctaaagtatactcctgttcttctctcccaccctaagtctcttttttacatacttgaattttatattaattgggtaacacattttaattttgtgcatgcagCTTGGTGAAACCATATATCCTATGAAGGAAGATTTCATTATGGTCCATTTGCAGTATTCATGTAGTCACTGCTGTACCCTTATGGTGTCTGGAAGACGTT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G139977_T01 (Zea mays), 3'ss of exon 11
---------------------------------------------------aaacattaatattgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttgataatttcttataaaattcttgatctt---tctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
||| | ||| | | | | || | | | | | ||| | || || ||| || | | || || | || || || | | ||||||||||||||||| | || |||||||||||||| |||||||| ||||| ||| || | |||| | |||||||| | ||||||||||| | ||||
gtaagcttctttgatttctgtgtacttcctgctctcataaataaatactcaaaaaaagtatactcctgcttctctctcccaccct-gtctcttttttacttgaattttgtatattgggcgacacatt-taccgtgctctattttgtgtatgcagCTTGGTGAAACCATATATCCTATGAAGGAAGATTTCATTATGGTCCATTTACAGTATTCGTGTAGTCACTGTTGTACCCTTATGGTGTCTGGAAGACGTT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G16710.1 (Arabidopsis thaliana), 3'ss of exon 12
--aaacattaatattgtttcctta---ctttactgctt------tcaaata-tttatctgttaggttccttatgtttgataatttcttataaaattcttgatctttct--ccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
| |||| | | | | || |||| |||| | | || || || | | || || || || | || | ||| ||| || | ||| | |||||||||| |||||| ||||||||||| |||||||| |||||||| ||||||||| || || || |||| | ||||| |||| || ||||
gtagtcatttctttctatgcactagtcctttcctgcatatcagcttaagtaattcgtttttttttttttttttgcctttgtgttcgtgttaatattatttctgtttgtgtttagCTTGGTGAGACCATTCATCCAATGAAGGAGGATTTTATCATGGTTCACTTGCAGCATAGTTGCACACATTGCTGTACGCTGATGGTAACTGGAAATCGTT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G55970.1 (Arabidopsis thaliana), 3'ss of exon 11
aaacattaatattgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttgataatttcttataaaattcttgatctttctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
|| || | || ||| || ||| | || || | | || | | | | | | ||||| |||| ||||| ||||||| || ||||||||||||||||| |||||||||||||| ||| || | ||| | | | ||||| ||||| ||||| |
-------------------gtaacttcttatttct--ccattccactattatgatc-ttgcttccaccagcttttatttatttgttctgtttttctgtagCTCGGTGAGACCATTTGTCCGATGAAGGAAGATTTTATAATGGTTCATTTGCAACATTGCTGCAAGCATTGTACCACTCTCATGGTATCTGGAAACCGGT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
lower sequence: AT3G12980.1 (Arabidopsis thaliana), 3'ss of exon 12
------------------------------aaacattaatattgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttgataatttcttataaaattcttgatcttt---ctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
| | |||| ||||||| | |||| | | ||| || || || | | | || || || || | ||||| || || |||| ||||| | ||| |||||||||||||||||| || |||||||||||||| ||| |||| ||||||| | | ||||| ||||| || ||||
gtaacttctttacctttaagttttccctttattcgttaactttgtttcactga--tactcttacctaatcttcatgcctttgttgaagaaagtgatattatcaaccccctaacttttgattgttactctgtagCTGGGTGAGATCATCCTCCCAATGAAGGAAGATTTCATCATGGTTCATTTGCAACATTGTTGTAAGCATTGTTGTACTCTCATGGTATCTGGAAATCGTT
upper sequence: GLYMA08G24290.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv09s0054g01780.t01 (Vitis vinifera), 3'ss of exon 11
----------aaacattaatattgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttgataatttcttataaaattcttgatctttctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
|| | ||||| | | | | | || |||| || | | || | ||| |||||| ||||||| || | | || |||||||||||||||||||||| ||||||||||||||||||||| |||||||| ||||| |||||||||||| |||||| | | ||||| ||||| |||||||
tttcaaacgtcttcactgatattatattttctcctgac-acttttgaacaaatgaaagtcaatttc----tgtttg-----ttcttatgaagctatctattcttctccagCTTGGTGAAACCATAAGCCCAATGAAGGAAGATTTTATAATGGTTCACTTGCAACATGCATGTACTCATTGTTGTCATCTGATGGTATCTGGAAACCGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttaggttccttatgtttgataatttcttataaaattcttgatctttctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
tcttgat putative branch site (score: 4)
ttcttgatctttctcc CT-rich tract
ttatgtttgataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaacattaatattgtttccttactttactgctttcaaatatttatctgttaggttccttatgtttgataatttcttataaaattcttgatctttctccagCTTGGTGAAACCATTTCCCCAATGAAGGAAGATTTTATTATGGTTCATTTGCAGCATGCATGTACTAGCTGTTGTATTTTAATGGTGTCTGGCAACCGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - tgtttcc
- - - - - - - - - - - - - - tgctttc
- - - - - - - - - - - - - - - - - - - - - - -ctgttag