Sequence
atgc intronic sequence ATGC exonic sequence...ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
Basic information
species | Glycine max |
transcript | GLYMA14G03290.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g35450.1 (Oryza sativa), 3'ss of exon 4
-----------------ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccc-cttagtgtactgtgattggtg-gcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
| | | | | | || ||| | | || || ||| | | ||| || |||||| || || |||||| |||||||||||||||||||||||||||||| ||||||||| | ||||||||||| || || ||||||||| | || ||||| |||||||||| || |||||
gtaagaaacaaaccatcgtccccgtcaaaaagaaaagaattgttc-ttcactttagctcttttat-atgtatat-gtttagttgcataacccattttccataactgaattggtatacagGCTTGCTTATTTACATGAAGCAATAGAGCCAAAAGTTGTACACCGGGATATCAAATCAAGCAACATACTAATCGATGAAGAATTCAATGGCAAACTTTCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g44110.1 (Oryza sativa), 3'ss of exon 5
ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
||| || | ||||| |||| | | || | || || | | | | | | || | | | || | ||| || ||||| | |||||||| ||||||||||||||| | ||||| |||||||| || ||||| || ||||||||||| ||||| |||| ||||| |||
---gtaagtttcatcagcttctcagtctataagatacatgttgtttctgttg--tcggaatttgtttgatgatattttggcgggttaatcatgatcacagACTAGCTTACCTTCATGAAGCTATAGAACCAAAAGTTGTGCACCGAGATATAAAATCAAGCAATATCTTGATTGATGAGGAATTTAATGGCAAGGTCTCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g47470.1 (Oryza sativa), 3'ss of exon 4
--------------------------ccagtagctt--agagtagcttagtcgtct-gttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
|||| || | | ||| | ||| | | | || || ||| | | || | ||| | || ||||| ||||||||| ||| | |||||||| ||||| || |||||| | ||||| ||||| ||||| || || ||| | |||||||||||||| || |||||||||
gtaagatcacagtctggaccttacttgcagttatttcccatgaaatttacccttctcacataaatacaggttttaaagatcaatacta--ctacatgctaatgtagatgagtttcatgatttt---cagGCTTGCATATCTTCATGAAGCTATAGACCCCAAAGTTGTACACCGAGATATTAAGTCAAGTAATATACTAATTGATGATGAATTTAACAGCAAGGTTTCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010953_T01 (Zea mays), 3'ss of exon 2
ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactg-tgattggtg-gcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
||| | | ||| | || | || | | | | | | | | | || ||| ||| | |||||||||||||||||||||||| ||||||||||||||| | ||||| ||||| || || ||||| || || |||||||| |||||||||| ||| |||||
-------------gtaagaaatgaaaccattcacaattttgcatcttttatatgcatacatttattaaattaagatgttgtctacaactgaacactatacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTACACCGTGATATCAAATCGAGCAATATCTTAATTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G026301_T01 (Zea mays), 3'ss of exon 4
ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtact--gtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
| | | | || || || || ||| ||||| | | ||| | | ||| | || | || | |||| |||||||||||||||||||||||| ||||||||||||||| | ||||| ||||| || |||||||| || | ||||||| |||||||||| ||| |||||
------gtaagacatggaccattcaatattttgtctc-----ttctttgatgcatat-gttttgccatctaaggcatttttataattgatgatatactacagGCTTGCTTATTTACATGAAGCCATAGAACCAAAAGTTGTGCACCGTGATATCAAATCTAGCAATATCCTAGTTGATGAAGAATTCAATGGCAAGCTTTCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G017386_T03 (Zea mays), 3'ss of exon 4
ccagtagcttagagtagcttagtc-gtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactg-tgat--tggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
||| || | | |||| || || ||| || || ||| || | | | | | | |||| | | || | || |||| ||||||||||||| | |||||||| || || ||||||||| | || || |||||||| || |||||||||||||||||||||||||| |||| || || |||
---gtaagtttcaat--cttaatctgtaagttacctacatagtttc--ctgtgtttttagctgtataaaattggttcttatttttctaattatgatggttgcagGCTTGCTTACCTTCATGAAGCTATTGAGCCAAAAGTTGTACATCGAGATATAAAATCAAGCAACATATTGATTGATGATGAATTTAATGGCAAAGTATCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G42960.1 (Arabidopsis thaliana), 3'ss of exon 3
-ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
||| | || | || |||| | | |||| | | | ||||||| | || | | | | | | | | | | | |||||||||||| || ||||||||||||||||||||||| | ||| | || ||||| | || || ||||||||||||||||| || |||||||| | |||
gtaagtggtttgaaacagtttag-cttttgttgg----atatgttcaatgcttgat-------tattaaaagggtctgcaatttg-tacaact--ttacagGCTTGCTTACTTGCATGAAGCAATAGAACCAAAAGTGGTCCACAGAGACATAAAAGCAAGTAATATATTGATTGATGATGAGTTTAATGCAAAACTCTCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G59110.1 (Arabidopsis thaliana), 3'ss of exon 4
-ccagtagcttagagtagcttagtcgtctgttcgtgt---caaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
||| | ||| | | || || | | | | || ||||| | ||| ||| || | |||||| ||| | ||||||||||||||||||||||||||||||||||||||| | ||| | || ||||| | ||||| || ||||||| ||||| |||||||||||| |||||
gtaagttgtttaaaatgtgactgttgttggaccttttacttgaaatttcaaaaacaactctttaaggggatattgacatgctc-tgtactacaatt--ttacagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTAGTCCACAGAGACATAAAAGCAAGCAATATCCTGATTGACGATGACTTCAATGCAAAGCTTTCT
upper sequence: GLYMA14G03290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g00310.t01 (Vitis vinifera), 3'ss of exon 5
ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttag--tgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
| | | || | | || || | ||| || ||| | || ||| || | | ||| | | ||| |||||||||| ||||| ||||| ||||||||||| |||||| |||| || || ||||| || |||||||| |||||||||||||| ||||||||||||||||||
--tattccattcagaactgaaatctactccagaactgaaattgaacatcttggtctttcacactttgaaaaagtcaaaaaaatgtttcatattgggttgcagGCTTGCCTATTTGCATGAGGCAATAGAACCGAAAGTTGTTCATCGAGACATAAAATCAAGCAACATCTTGATTGATGATGAGTTCAATGCAAAGGTTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
gattaac putative branch site (score: 2)
tgattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccagtagcttagagtagcttagtcgtctgttcgtgtcaaagattcaatgatggaccttgttctcctgattaaccccttagtgtactgtgattggtggcagGCTTGCTTATTTACATGAAGCAATAGAACCAAAAGTTATTCACCGGGATATAAAGTCTAGCAACATATTGATTGATGATGAATTCAATGCAAAGGTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - gtctgtt
- - - - - - - - - - - - - - - - - - - - - - - atgatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acccctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tactgtg