Sequence
atgc intronic sequence ATGC exonic sequencegttatttgtgaagttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacattatagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA
Basic information
species | Glycine max |
transcript | GLYMA09G39560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G00460.1 (Arabidopsis thaliana), 3'ss of exon 2
gttatttgtgaagttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacattatagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
|| | || || | ||| | || | || | | | | | || || | | || || || ||||| |||||||||||||| || |||||||| || |||||||| ||||| || ||||| ||||| |||||||||||||| || ||||||||
-gtact-gtagttttctctctttctttcttctctgttttctt-ctactgctttttttaaatgtctcatgtgttctagggtttgtgcagAACTTGAGACAATGAAGGAAAGATTCGCTAAGCTTCTACTTGGAGAAGATATGTCAGGGAGTGGTAAAGGAGTTTGCACTGCAGTGACTATCTCAAACGC
upper sequence: GLYMA09G39560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G45890.1 (Arabidopsis thaliana), 3'ss of exon 1
gttatttgtgaagttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacatt---atagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
|||| | | |||| || |||| | || | || || || || | || ||||| || |||||| |||||||||||| ||||| |||| || ||||||||||| |||||||||||||| ||||| ||||| ||||| | |||||
-------------------------gtaaagtgtttaagattgtaactttcttcttttgtc-atttcgttaaatcggggtttctagtgcagAGCTAGAGATGATGAGGGAAAGATTTGCGAAGCTGTTGCTTGGTGAAGACATGTCAGGAAGTGGGAAAGGAGTTTGTACTGCTGTTACTGTGTCAAACTC
upper sequence: GLYMA09G39560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G01700.1 (Arabidopsis thaliana), 3'ss of exon 1
gttatttgtgaa---gttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacattatagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
||| | ||| || | || || | | || | || || | | | || || | |||| ||||| || ||||||||||||||| | ||||||||||| || ||||| ||||| ||||| || ||||| |||||||| ||||| |||||||||||
gttttgtgtttctccgtctctctctctttctctgtgtctgtatttcctctttgtcattataatcatgaaactgttatcggtttcgtagcagAGCTGGAGACGATGAAGGAAAGATTCTCGAAGCTTCTGCTTGGGGAAGATATGTCAGGAAGCGGCAAAGGCGTTTGCACCGCAGTGACAATCTCAAACGC
upper sequence: GLYMA09G39560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02530.t01 (Vitis vinifera), 3'ss of exon 1
gttatttgtgaagttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacattat--agCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
||| | || || | | | ||| || || || ||| || | | || || ||||||||| ||||||||||||||||| | |||||| |||| || ||||||||||| ||||| || ||||| || |||||||| || |||||||||||
-------gtgggtccaaacctcatttccggggaagctaaggtctggattctaatc-tgcttaactaacttgtatttgattttctgggcagAGCTTGAACTGATGAAGGAAAGATTTTCCAAGCTTTTGCTGGGTGAAGACATGTCAGGAAGCGGCAAAGGCGTCTGCACTGCGGTCACAATCTCAAATGC
upper sequence: GLYMA09G39560.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S28_109V6.1 (Physcomitrella patens), 3'ss of exon 2
-----gttatttgtgaagttttaggacacttagaagtttgaatgattacaa-atttcgatagtggttgact--tgattttgtccacattata-----gCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA---
| || || || | || | ||||| | ||||| | | | ||| | | || || || || | | || | || |||||||||| | ||||||||||||||||| || || || |||||||| | || ||||||||||||||||| | | || || ||
ggtctgctaccaagcgagcttcctaccg-ttgcacatttgaccagccattttatttcagttgcgagtgattgttatttctgattactttttgcttctacagAAGTGGAGATGATGAAGGAGAAGTTTGCAAAGCTTCTGCTTGGGGAGGATATGTCTGGTGGGGGAAAAGGTGTTTGCACTGCGTTGGCTATATCGAACTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttgaatgattacaaatttcgatagtggttgacttgattttgtccacattatagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA
ttttgtcc CT-rich tract
aatgattacaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttatttgtgaagttttaggacacttagaagtttgaatgattacaaatttcgatagtggttgacttgattttgtccacattatagCCGAGCTTGAATTGATGAAGGAAAGATTTGCAAAGCTTCTGCTCGGAGAAGACATGTCTGGAAGTGGGAAAGGTGTTTGCACTGCAGTTACAATCTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG