Sequence
atgc intronic sequence ATGC exonic sequence...tcatccatccatgaatgccttttagtgtgaaagattaaagtgcagaatttcagtttactaatattgcagcttgatacttttttctcttctgcatttacagCTAAGTACCCCCAAGGTCGATGCTTTGTGCGACCATCTGGCACTGAAGATGTTGTTCGTGTGTATGCTGAGGCATCCACACAGGAAGCAGCTGAGACACT
Basic information
species | Glycine max |
transcript | GLYMA01G40950.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G40950.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os07g09720.1 (Oryza sativa), 3'ss of exon 7
tcatccatccatgaatgccttttagtgtgaaagattaaagtg-----cagaatttcagtttactaatattgcagcttgatacttttttctcttctgcatt----tacagCTAAGTACCCCCAAGGTCGATGCTTTGTGCGACCATCTGGCACTGAAGATGTTGTTCGTGTGTATGCTGAGGCATCCACACAGGAAGCAGCTGAGACACT
| | | || | || | || | | | || | || | | ||| || | | |||| || | ||||| | | |||| || ||| | || || ||||| || ||||| |||||||| || || ||||| || ||||| ||||| |||||||| || ||||||||||||| ||
----gtaagtaacatcttctctgagcatataatacttatgtttctttccgacatccgattttct--tggcataaattgaagtgttactgaattctgaggtaccctgcagCAAATTACTCTCATGGGCGATGTTTCGTGCGGCCATCTGGTACCGAGGATGTGGTGCGTGTATATGCAGAGGCATCTTCAGAGGAAGCAGCTGATTGCCT
upper sequence: GLYMA01G40950.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G166597_T01 (Zea mays), 3'ss of exon 8
-------------tcatccatccatgaatgccttttagtgtgaaagattaaagtgcagaatttcagtttacta----atattgcagcttgatacttttttctcttctgcatttacagCTAAGTACCCCCAAGGTCGATGCTTTGTGCGACCATCTGGCACTGAAGATGTTGTTCGTGTGTATGCTGAGGCATCCACACAGGAAGCAGCTGAGACACT
|||| |||| | || | | | || || || | ||||||| || || || ||| || || | || | |||| || ||| |||| || |||||||||||||| ||||| || || |||||||| || || ||||| || |||||||| || |||| || |||||| ||
gtaagtaccaacttcattatgtcatgca-gcgtgtgacagttctgcatcgctaccttgaggtctgatttactatgcggtagtgtgact-gatgctcaaatcgcgatgtcact-gcagCCAACTACACCCACGGGCGATGCTTTGTGCGTCCATCCGGTACAGAAGATGTGGTACGGGTGTACGCAGAGGCATCTACGCAGGTAGAAGCTGACGGTCT
upper sequence: GLYMA01G40950.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S211_20V6.1 (Physcomitrella patens), 3'ss of exon 8
tcatccatccatgaatgccttttagtgtgaaagatta--aagtgcagaatttcagtttactaatattgcagcttgat-------acttttt----------------tctcttctgcat-ttacagCTAAGTACCCCCAAGGTCGATGCTTTGTGCGACCATCTGGCACTGAAGATGTTGTTCGTGTGTATGCTGAGGCATCCACACAGGAAGCAGCTGAGACACT
|| ||| | ||| |||||||| || || || | || | | ||| | | | |||||| |||||| |||| | || || | ||| ||||| ||| | |||||||||||||| || || ||||| || ||||| |||||||||||||| |||||| || ||||| | |
gtgagtatttgcgaaagatgtttggtgtgaaacttttctaactgagcagcgtctgctccgtaacacag-accttgatttcaagtacttttaggaaattcacaccctatctcatttggatgctgcagAGAAGTATGAGGGAGGAAGGGCTTTTGTGCGACCATCAGGAACCGAAGACGTGGTTCGGGTGTATGCTGAGGCTCAGACACAGAAAATCGCTGATTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatttcagtttactaatattgcagcttgatacttttttctcttctgcatttacagCTAAGTACCCCCAAGGTCGATGCTTTGTGCGACCATCTGGCACTGAAGATGTTGTTCGTGTGTATGCTGAGGCATCCACACAGGAAGCAGCTGAGACACT
tacttttttctcttct CT-rich tract
agtttactaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcatccatccatgaatgccttttagtgtgaaagattaaagtgcagaatttcagtttactaatattgcagcttgatacttttttctcttctgcatttacagCTAAGTACCCCCAAGGTCGATGCTTTGTGCGACCATCTGGCACTGAAGATGTTGTTCGTGTGTATGCTGAGGCATCCACACAGGAAGCAGCTGAGACACT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- -tccatcc
- - - - - - gaatgcc
- - - - - - - - - - - tagtgtg
- - - - - - - - - - - - - - - - - - aaagtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tattgca