Sequence
atgc intronic sequence ATGC exonic sequence...aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcctctttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
Basic information
species | Glycine max |
transcript | GLYMA13G28730.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g30870.1 (Oryza sativa), 3'ss of exon 2
-aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcctctttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|||| | || | || | |||| || ||| | || || || | | | || | ||||| | | |||||| ||||| || || || ||||| || ||||| |||||||||||| |||||||| |||| ||||| |||||||||||||| ||||| ||| || || |
atggttactgcatttcttttaaccccctatgtgatctgtggagcattagaggagacatgtttccttaa-agtcttgatcgatgagcttaccaaatatgcagGCTGTTGCAGTGAAGCAACTTGATCGCAATGGACTTCAAGGAAATAGAGAGTTTCTGGTTGAAGTCCTTATGCTCAGTCTATTGCACCATGATAACCTGG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
-aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcctct-ttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| || | || | || || | ||||| | || || || || | || |||||| | || | | |||||| ||||| || ||||||||||| | |||||| ||||| ||||| |||| || | ||||| ||||| ||||||||||||||||||||||| ||| | |
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaattt--ggttccagcatttgctgcatcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g47270.1 (Oryza sativa), 3'ss of exon 2
-------aagttatctgtctgct-ctcaattttcctgttgatta-ttgctctgtt-actataactctgcct--ctttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| | ||| || | || |||| |||| ||| | | | || | | | | | | | ||| | || | || || | |||||| |||| || || || |||||| ||||||| || |||||||| ||||| ||| | ||||| ||||| ||||| ||||||||||| ||||| ||||| |
gtttgctattcctaacattggctgctgtgtgctcttgttcattagctgcaatttagagcatgatttttctgagtgtccgacaccttttcttttgcatatatcatc-tagcagGTTATTGCCGTGAAGCAACTTGACAGAAATGGCCTACAAGGAAACCGAGAATTTCTCGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g71000.1 (Oryza sativa), 3'ss of exon 2
----------------------------------------------aagttatctgtctgctctca---attttcctgttgattattgctctgttactataactctgcctctttcataatttttaa----tgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| | | | | | | ||| |||| | | | | | |||| | || | | | || | | | ||||||| | | | |||| |||||||| || || ||||| || |||||||||||||||||| |||| || |||| || || || ||||||||||| | ||||| | || || |
gtcagtctttcttaacctatctagatctattgagattttactaaatacttgaagtttaggttttcagcgatttagttaatattcagtaaaatgttggcagaattgctgttttgctttatccctggagcactaatgaaatataccacttcccagGCTGTTGCTGTGAAGCAACTTGATCGCAATGGTCTTCAAGGAAATAGAGAATTCCTGGTTGAGGTCCTCATGCTCAGTCTTCTACATCACACTAACCTGG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G048210_T02 (Zea mays), 3'ss of exon 2
---------------------------------------------aagttatctgtctgctctcaattttcctg---ttgattattgctctgt-tactataact--ctgcctctttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|| || | | ||||| | || | | | ||| | | ||| | || | | | | || | || ||| | |||| ||||||| || || ||||| |||||||| ||||||||||||| || ||| | ||||| ||||| ||||| ||||||||||| ||||| ||||| |
gtttgctaacatttgctgattgtgttgtaatttctgtacactgcaaatttggatataaagtctcattaagaagaaaagggagaagtcccctgagtgttctaattggttgattgcctgacaccttcgtttttcatcttctatcttgc-atagGTCATTGCTGTGAAGCAACTTGATAGAAATGGTTTTCAAGGAAATCGTGAATTTCTTGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------aagttatctgtctgctctcaattttcctgttgattattg-----ctctgttactataac--------tctgcctctttcataatttttaatgatgaaatcattct-cgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|| || |||| | || | || | ||||| || || ||||| | | || || | | || | | | || | | | |||| |||||||| ||||| ||||| || |||||||| |||||||| | || ||| |||| || ||||| |||||||||||||| ||||| | || || |
gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagccctggattagtcctggatactaacagagttttacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G177061_T01 (Zea mays), 3'ss of exon 1
---------------------------------------------aagttatctgtctgctctcaattttcct----gttgattattgctctgt-tactataact--ctgcctctttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|| || | | ||||| | || | | | ||| | | ||| | || | | | | || | || ||| | |||| ||||||| || || ||||| |||||||| ||||||||||||| || || | ||||| ||||| ||||| ||||||||||| ||||| ||||| |
gtttgctaacatttgctgattgtgttgtaatttctgtacactgcaaatttggatatagagtctcattaagaagaaaaagggagaagtcccctgagtgttctaattggttgattgcctgacaccttcgtttttcatcttctatcttgc-atagGTCATTGCTGTGAAGCAACTTGATAGAAATGGTTTTCAAGGAAATCGTGAATTCCTTGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G037585_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------aagttatctgtctgctctcaattttcctgttgattattgctc-----tgttactataac-------tctgcctctttcat-aatttttaatgatgaaatcattct-cgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|| || |||| | || | || | | ||| | || || ||||| ||| | | || | | || | | | || | | | |||| |||||||| || || ||||| || ||||| || ||||||||| | || ||| |||| || ||||| |||||||||||||| ||||| | || || |
gtaagcatatctgaaacatgacgcattgacattttgattgtaaagctaaatcctctcaaatttggcttctgagttgaaacattaagtaaaatgttggtgggaaatgctaacataacgattatacttgcgccctggattagccctggatactaacagagttttacttcccagGCTGTTGCTGTGAAGCAACTTGATCGTAATGGCCTCCAAGGAAATAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3
aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcctctttcataatt-tttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
||| | | | | | ||| | | | | | | | | | | || || |||||| |||| ||||| ||||||||||| ||||| ||||| |||||||| |||||||| | || || ||||||||||| || || |||||||||| |||||||
-----------------------------gtgaagttcgtaaattgaatttaatgtttcataatcaagattcgtcttctaattggatttaatattttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
upper sequence: GLYMA13G28730.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcc--tctttcataatttttaatg-atgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| | | | | | | | | || ||| || || | | ||| | ||| | | ||| | |||||| | | ||| ||| | ||||||||||||||||| ||||| |||||||||||||| |||||||||||| |||| || |||||||| ||||| ||||| || ||||| ||||| ||||| ||||
-aatcttttatata-tggaatatggattgctgaataatg-ttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactataactctgcctctttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
ttttaat putative branch site (score: 3)
tcattctc putative PPT
tttcataatttttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagttatctgtctgctctcaattttcctgttgattattgctctgttactataactctgcctctttcataatttttaatgatgaaatcattctcgttgcagGTAGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - -ctgctct
- - - - - - - - - - - - -cctgttg
- - - - - - - - - - - - - - - - - - -tgctctg