Sequence
atgc intronic sequence ATGC exonic sequence...ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
Basic information
species | Glycine max |
transcript | GLYMA12G04290.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 2
---------ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
|| | || | | | ||| || ||||| | | |||||| | | | || || | | ||| |||| ||||||| ||||| |||||||| |||||| || | ||||||||||||||||| ||||| || ||||||||||| || || |||||||||||||| || || ||
attgctagactggccaaacacaaaactatatgcatatgcagcaaaccgct---attgaggtatttgaattaatgtaatctaaatg--tgctatttttttgga----cagACACGAAGGCTTGGGAAGTTGATACTTTGCGGGGACACATGAATAATGTGTCATGCGTGATGTTCCATGCTAAGCAAGACATCATTGTGTCCAACTCAGA
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g04110.1 (Oryza sativa), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtc-cctaatatat-tttcccgtttt----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
| | | | || ||| | | |||| || | | | || | ||| | | || | ||| || | | | |||| ||||||||||||| |||||||| |||||| || | || |||||||||||||| || || || ||||||||||| || || |||||||||||||| || || ||
----tattctactgcacattggtag-actggccaaacgctattatatgca-taccactattgaggtatttgaaatgatgcaatctaagtgtgctatttttggacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAATGTGTCCTGCGTGATGTTCCATGCAAAGCAAGACATCATTGTGTCCAACTCAGA
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtt-tagtatttttggtgaccttct-caaagtccctaatatattttcccgtttt-cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
| | | | | ||| | | | | | || | ||||| | || | | | | || | | ||| ||||||||||||| |||||||| |||||| || | || ||||||||||| || || ||||| ||||||||||| || || |||||||| ||||| || || ||
---gcaaactttgtggggtgtggaacattcacttccactatcaccattgcattatttaaagggataataggtgatgcaatctaaatgtgctgttttttgacagACACCAAGGCTTGGGAAGTTGATACTTTGCGGGGGCACATGAATAACGTGTCCTGTGTGATGTTCCATGCAAAGCAAGACATCATAGTGTCCAACTCAGA
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G010054_T01 (Zea mays), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaac--caaataaagtttagtatttttggtgaccttctcaaagtccc-taatatat-----tttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
||| ||| || || |||||| |||| | | ||| | ||| || | | || | | || | | |||| ||| || | |||| |||||||| |||||||| |||||| | || || |||||||||||||| || ||||| ||||||||||| || || |||||||| |||||||| || ||
--tttagcag--atcaa----ttagtacttagcatatgtgaaaaagagtatacattctacaaggaaatgtttgaaatgcaataatctatatgtgttctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGCCACATGAATAATGTGTCTTGTGTGATGTTCCATGCGAAGCAAGACATCATCGTGTCAAACTCAGA
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G149406_T01 (Zea mays), 3'ss of exon 2
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgtttt-----cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
||| | || | | | ||| || | ||| | ||| | || | | | | | || | |||| ||| | | ||| |||| |||||||| |||||||| |||||| | || || ||| |||||||||| || ||||| ||||||||||| || || |||||||||||||| || || ||
-tttagctgttcaattagtacctagcatatgtgaaagaatatatacatt----ctacaaggaaatatttggaatgcaataatttatgtctgctctttatggacagATACCAAGGCTTGGGAAGTTGATACTTTAAGGGGTCACGTGAATAATGTGTCCTGTGTGATGTTCCATGCGAAGCAAGACATCATTGTGTCTAACTCAGA
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------ctttttgcatgc-attaactttttagtatttagtaaaccaaataaagtttagtat---------ttttggtgaccttctcaa-----------agtccctaatatattttc--ccgt----tttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
||||| |||| || || | | || | | | || || | || || | ||| || || ||| ||| || |||| | | || |||| || || || ||||| |||||||| || |||| || |||||||| ||||||| ||||||||||||||| ||||||||||| ||||| ||||| |||||
gtaattatttggtggtatacttttgtgcttacaatttttatatgctatcaatcgtcaatgatgttactgatatgaaaatattctgcatgccttaatccttagatgaatctcgaaattgcaaagacgagttggtaacatgtttttaacgatatcattgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGCCATATGAATAACGTTTCATCTGTTATGTTCCATGCAAAACAGGACATAATTGTATCAAACTCTGA
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 3
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgtttt--cagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
| ||| ||| | ||| | | || || |||| | | | || || || ||| || | |||| || || || ||||| |||||||| || |||| || |||||||| ||||||| |||||||||||||| ||||||||||| || |||||||| |||||
----------gtattt-cttatggatatctgtcttcttcttcacagaaagttaattttatgaatcatt---gaggtactgatgcgtttcaattttgttgcagAAACTAAAGCTTGGGAGGTGGATACATTGCGAGGTCATATGAATAACGTTTCATCCGTTATGTTCCATGCAAAACAGGACATTATCGTGTCAAACTCTGA
upper sequence: GLYMA12G04290.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv18s0001g13430.t01 (Vitis vinifera), 3'ss of exon 3
ctttttgcatgcattaacttt-ttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatat-tttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
|| | ||| |||| | || ||| || | ||| | || ||| ||| || || | || || || ||| | |||||||||| ||||| |||||||| |||||| |||| || ||||||||||||||||||||||| | || ||||| | ||||| | |||||||||||||| ||
tttcatccatttgttaatcgtattttctttttgttagggttatagaactttgtagaattga--actagctaatggtttgcaacttaccttttctactttcagACACAAAGGCTTGGGAAGTAGATACTTTGAGGGGGCACATGAATAATGTTTCATGTGTCTTCTTTCATGCAAGGCAGGATGTGATTGTGTCAAATTCAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttagtatttttggtgaccttctcaaagtccctaatatattttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
ccctaat putative branch site (score: 3)
tattttcccgttttc CT-rich tract
taatatatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctttttgcatgcattaactttttagtatttagtaaaccaaataaagtttagtatttttggtgaccttctcaaagtccctaatatattttcccgttttcagACACCAAGGCATGGGAAGTGGATACTCTGAGAGGACACATGAATAATGTTTCATGTGTTATGTTCCATGCCAAACAGGACATCATTGTGTCAAATTCTGA
- - - gcatgca
- - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tttggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtccct