Sequence
atgc intronic sequence ATGC exonic sequence...ttatttatgctttcaaatgcttgaagtttttgtttggctgttgttttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
Basic information
species | Glycine max |
transcript | GLYMA04G39500.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g56100.1 (Oryza sativa), 3'ss of exon 3
-ttatttatgctttcaaatgcttgaagtttttgtttggctgttgttttttcgtatgtgatga-aataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
|| || || | || | || | | | | || || | |||| | || ||| || || ||| ||| | || || ||||| | | || | |||||||||||||| ||||||||||| ||||||||||| || ||||| || || ||||||||||| ||||| || || || |||
atttcttgtgtggatatatttcttcaggtgct--tcaattttttattatatgtatattgtgccaatgtgacttgataatttctatatgatgcaccatttcagAATACCACCCGCTTGGACAGTGAGATAATTTATGACAGAGATTTTGACTATGACTACTTTGGTTTTAAGACCCTTGAGAGATCTTATCTGTTAAAAGTTG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g07210.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------ttatttatgctttcaaatgcttgaagtttttgtttggctgtt--gttttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
| |||| | | | || | | || |||| || | || || | | || | | | || | || | | | || || |||||||| |||| | ||||| |||||||| ||||| || ||||| || |||||||||||||| ||||| || || ||||||||||||||| |||| ||
gtgagatatcaaattaaactttagggacttgcactgatagctgttcttgttctgatttgtaaaatttactgttccattcaatttattggtcattaggattattgatgtatgttatgcttcttacggtttctgatgttctgatccttattttcagAATGCTTCTCGCTTGGACAGCGAGATAATTTATGATAGGGACTTCGATTATGATTATTTTGGTTTCAAGACTCTGGAGAGGTCTTACCTCCTGAAACTTG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G340527_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------------------------------ttatttatgctttcaaatgcttgaagtttttgtttggctgttgttttttcgtatgtgatg-aaataatcttttat-tattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
||||| | | | | | | | ||| | | | | || || || | ||||| |||| | | || | | | |||| || ||||||||||||| | |||||||| ||||| ||||| || || || |||||||| || ||||| |||||||| || ||||||||||||||||||||| ||
gtgagattctagttgctcctggcacatttctgacagagcatctgtgtagataatgccgatgtgtttctggcagttgaatttactgttgcattcctttttttattaaggttgtttatctcatacagtaaatctgttg-tgcccttcactcacct-tgatgtaaattggccctcatatcgctccaaatgctgttacatttcagAATGCTGCTCGCTTGGACAGTGAAATAATTTATGATAGGGATTTCGACTATGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTCTTGAAGCTTG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G304362_T01 (Zea mays), 3'ss of exon 3
ttatttatgctt-tcaaatgcttgaagtttttgtttggctgttgttttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
| || || || || | || | | | | || | ||| || | | | | | | |||| || ||||||||||||| | |||||||||||||| ||||| || || || ||||| || || ||||| |||||||| || |||||||||||||| |||||| ||
acaaggctgtttatctcatacagtaaatctgt-tgtgccccgcacaacacaccttgttggaaattggccctcacatgactccaaatgatgttacatttcagAATGCTGCTCGCTTGGACAGTGAGATAATTTATGATAGGGATTTCGACTACGACTACTTTGGCTTCAAAACTCTGGAGAGGTCTTACCTGTTGAAGCTTG
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv07s0031g01990.t01 (Vitis vinifera), 3'ss of exon 3
----ttatttatgctttcaaatgcttgaagtttttgtttgg--ctgttgttttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
| | | | || ||||| | | | | || || | || | || ||| | | | ||||| || || || |||||||||||||| | |||||||| || || |||||| | |||||||| |||||||| ||||| |||||||||||||||||||| |||||| ||||| |||
ctggtggtgtgcatgtctggat-cttgacttggaaatatagaattgctggtccttgacacaaatctcaacaattctatttgtttatttcttctttctt-----cagAATGCTGCTCGTTTGGACAGTGAAATCATTTATGACCGGGACTTTGATTATGATTACTTTGGTTTCAAAACCCTTGAGAGGTCCTACCTCCTGAAGATTC
upper sequence: GLYMA04G39500.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S64_38V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------ttatttatgctttcaaatgcttgaagtttttgtttggctgttgttttttcgt-atgtgatgaaataatcttttattattattattttttgtttgg--ttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
|| ||| | || || | | |||| || | || | || | | | | ||| | || ||| ||||||||||| | || || ||||| ||||| || |||||||| ||||||||||| ||||| ||||| ||||| || | ||||| ||||| || |||| |||
gtacgactgatgatttgaatatcagaacgaactctccttcctgggatacaatccacgtttcatcttcatttcttgcgcgtgccctctgtc-ttacagcgctatgcttgtctttgtagAATGCCCCGCGCCTGGACAGCGAGATTATATATGACAGGGACTTTGACTACGATTACTTTGGCTTCAAGACATTAGAGAGATCTTATCTTCTGAAAGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
ttttttgttt CT-rich tract
tatgtgatgaaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatttatgctttcaaatgcttgaagtttttgtttggctgttgttttttcgtatgtgatgaaataatcttttattattattattttttgtttggttgtagAATGCTGCTCGTCTAGACAGTGAGATAATCTATGACAGAGACTTTGACTATGATTATTTTGGATTCAAAACCCTTGAGAGGTCTTACCTCTTGAAGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - -tgctttc
- - - - - - - - -tgcttga
- - - - - - - - - - - - - - - - -ttggctg
- - - - - - - - - - - - - - - - - - - - - - - - - gtatgtg