Sequence
atgc intronic sequence ATGC exonic sequence...tgtgtgtgtgtggtgtatttgttggttgtgtgattttgtttgactgttgttttggtatgatttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
Basic information
species | Glycine max |
transcript | GLYMA08G15360.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 3
--tgtgtgtgtgtggtgtatttgtt--ggttgtgtgattttgtttgactgttgttttggtatgatttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
| |||||| | | ||||| || ||| | ||||| | | | | | ||| || ||| || | || | | | | || ||| ||||| | || ||||||||||||||||| ||||| ||||| ||||||||||| ||||||||||| || ||||||||||| || || | | || |||
atttcttgtgtg-gatatatttcttcaggtgcttcaattttttattatatgtatattgtgccaatgtgac-ttgataatt--tctatatgatgcaccatttcagAATACCACCCGCTTGGACAGTGAGATAATTTATGACAGAGATTTTGACTATGACTACTTTGGTTTTAAGACCCTTGAGAGATCTTATCTGTTAAAAGTTG
upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 3
-----------------------------------------------tgtgtgtgtgtggtgtatttgttggttgtgtgattttgtttg-----actgttgttttggtatgatttgaaattcacg-tttgttttgttttctgttttgtttt-agAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
||| | || |||| || | | | ||| || | | || || ||||| | || | ||| ||| | |||| | || |||| |||||| | |||| |||||||| |||||||| |||||||| ||||| || |||||||| ||||||||||| || || |||||||| ||| ||||||| ||
gtgagatatcaaattaaactttagggacttgcactgatagctgttcttgttctgatttgtaaaatttactgttccattcaatttattggtcattaggattattgatgtatgttatgcttcttacggtttctgatgttctgatccttattttcagAATGCTTCTCGCTTGGACAGCGAGATAATTTATGATAGGGACTTCGATTATGATTATTTTGGTTTCAAGACTCTGGAGAGGTCTTACCTCCTGAAACTTG
upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------------------tgtgtgtgtgtggtgtatttgt-tggttgtgtgattttgtttgactgtt-----gttttggtatgatttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
| | | | | | | ||| | | | || | | |||| | || ||| | | | ||| ||| | | | | ||||| ||| |||||| |||||| ||||||||||| ||||| |||||||| || || |||||||| |||||||| |||||||| || |||||||| ||| || ||||| ||
gtgagattctagttgctcctggcacatttctgacagagcatctgtgtagataatgccgatgtgtttctggcagttgaatttactgttgcattcctttttttattaaggttgtttatctcatacagtaaatctgttgtgcccttcactcaccttgatgtaaattggccctcatatc-gctccaaatgctgttacatttcagAATGCTGCTCGCTTGGACAGTGAAATAATTTATGATAGGGATTTCGACTATGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTCTTGAAGCTTG
upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
-tgtgtgtgtgtggtgtatttgttggttgtgtgattttgtttgactgttgttttggtatgatttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
| ||| | || | | ||| | ||| | | ||| |||| | | | |||| ||| |||||| |||||| ||||||||||||||||| |||||||| || || ||||| || |||||||| |||||||| || |||||||| ||| | ||||| ||
acaaggctgtttatctcatacagtaaatctgttgtgccccgcacaacacaccttgttggaaattggccctcacatg-actccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
-tgtgtgtgtgtg-gtgtatttgttggttgtgtgattttgtttgactgttgttttggtatga--tttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
|| ||||| || | | ||| | | || | | | ||| | ||| | | | | | | ||||||| || | | || || |||||| |||||| ||||||||||| || || ||||| | |||||||| ||||||||||||||||||||||||||||||||||| ||| |||||||| |||
ctggtggtgtgcatgtctggatcttgacttggaaatatagaattgctggt-ccttgacacaaatctcaacaattctatttgtttatttct---tctttcttcagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
upper sequence: GLYMA08G15360.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 2
-------------tgtgtgtgtgtggtgtatttgttggttgtgtgattttgtttgactgttgttttggtatgatttgaaattcacgtttgtttt-----gttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
| || | | | | | | | || ||| | | | | || || ||| | | | ||| || | | | | | || ||||||| | || ||||||| ||||| || ||||| || ||||||||||| ||||||||||| ||||| || | ||||| || || | ||||| |||
gtacgactgatgatttgaatatcagaacgaactctccttcctgggatacaatccacgtttcatctt--catttcttgcgcgtgccctctgtcttacagcgctatgcttgtctttgtagAATGCCCCGCGCCTGGACAGCGAGATTATATATGACAGGGACTTTGACTACGATTACTTTGGCTTCAAGACATTAGAGAGATCTTATCTTCTGAAAGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgttttggtatgatttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
ttttgttttctgtttt CT-rich tract
tatgatttgaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgtgtgtgtggtgtatttgttggttgtgtgattttgtttgactgttgttttggtatgatttgaaattcacgtttgttttgttttctgttttgttttagAATGTTGCTCGATTGGACAGTGAGATAATCTATGATAGAGACTTTGACTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCATACATCCTGAAGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
-gtgtgtg
- - - - - - - - - - - -ggttgtg
- - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - actgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attcacg