Sequence
atgc intronic sequence ATGC exonic sequence...aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
Basic information
| species | Glycine max |
| transcript | GLYMA15G10360.1 |
| intron # | 2 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g15470.3 (Oryza sativa), 3'ss of exon 2
-aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| || | || || || || | ||||| | || || || || | | | || || | | | | | |||||||| ||||| || ||||||||||| | |||||| ||||| ||||| |||| || | ||||| ||||| ||||||||||||||||||||||| ||| | |
atgggaatgcttagactattgatgttaacagaaagtattgttatgctatataccctttgtataaatttctaatttggttccagcatttgctg-catcgcagGTTGTTGCAGTTAAACAGCTTGATCTAAATGGGCTTCAGGGAAACAGAGAATTCCTTGTGGAGGTTCTCATGCTCAGTCTCTTGCATCATCCTAATTTAG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g30870.1 (Oryza sativa), 3'ss of exon 2
-aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|||| | | || || | |||| || ||| | ||| || || | |||| || |||| | | | ||||| ||||| || || || ||||| || ||||| |||||||||||| |||||||| |||| ||||| |||||||||||||| ||||| ||| || || |
atggttactgcatttcttttaaccccctatgtgatctgtggagcattagaggagacatgtttccttaa-agtcttgatcgatgagcttaccaaatatgcagGCTGTTGCAGTGAAGCAACTTGATCGCAATGGACTTCAAGGAAATAGAGAGTTTCTGGTTGAAGTCCTTATGCTCAGTCTATTGCACCATGATAACCTGG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g47270.1 (Oryza sativa), 3'ss of exon 2
---------aagttat-ttgtctgctggaaatttt--cccattgattattgctctgttactataactatgcct--ctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| | ||| |||||| | | |||| | | | | || | | | | | || | ||| | || | || ||| |||||| |||| || || || |||||| ||||||| || |||||||| ||||| ||| | ||||| ||||| ||||| ||||||||||| ||||| ||||| |
gtttgctattcctaacattggctgctgtgtgctcttgttcattagctgcaatttag--agcatgatttttctgagtgtccgacaccttttcttttgcatatatcatcta-gcagGTTATTGCCGTGAAGCAACTTGACAGAAATGGCCTACAAGGAAACCGAGAATTTCTCGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g71000.1 (Oryza sativa), 3'ss of exon 2
---------------------------------------------------aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatctt----cattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
||||| | | | | |||| | | | | | |||| | || | | | || | | || ||||||||| | |||| |||| |||||||| || || ||||| || |||||||||||||||||| |||| || |||| || || || ||||||||||| | ||||| | || || |
gtcagtctttcttaacctatctagatctattgagattttactaaatacttgaagtt--taggttttcagcgatttagttaatattcagtaaaatgttggcagaattgctgttttgctttatccctggagcactaatgaaatataccacttcccagGCTGTTGCTGTGAAGCAACTTGATCGCAATGGTCTTCAAGGAAATAGAGAATTCCTGGTTGAGGTCCTCATGCTCAGTCTTCTACATCACACTAACCTGG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G048210_T02 (Zea mays), 3'ss of exon 2
--------------------------aagttatttgtctgctggaaattt----------tcccatt------------gattattgctctgt-tactataacta-tgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| | ||| ||| |||||| || |||| || | | | ||| | | ||| | | | | | |||| || | | | | | | |||| ||||||| || || ||||| |||||||| ||||||||||||| || ||| | ||||| ||||| ||||| ||||||||||| ||||| ||||| |
gtttgctaacatttgctgattgtgttgtaatttctgtacactgcaaatttggatataaagtctcattaagaagaaaagggagaagtcccctgagtgttctaattggttgattgcctgacaccttcgtttttcatcttctatcttgcatagGTCATTGCTGTGAAGCAACTTGATAGAAATGGTTTTCAAGGAAATCGTGAATTTCTTGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G145709_T01 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------------aagttatttgtctgctggaaattttcccattgattattgctctg-ttactataactatgcctctttcgtaatcttcattaatgaaatcattct-cttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|||| | |||| || | | | | | | |||| || ||| || || || | || | | | || | |||| |||| |||||||| ||||| ||||| || |||||||| |||||||| | || ||| |||| || ||||| |||||||||||||| ||||| | || || |
gtaagtatctcttaaacatgatgcatcgacattttatctgtgaagctaaatccttccaaatttggcttctgagttgaaacattaagtaaaatattggaaggaaatgctaacataacgattatacttaagcc-ctggattagtcctggatactaacagagttttacttcccagGCTGTTGCTGTGAAACAACTTGATCGTAATGGTCTCCAAGGAAACAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G177061_T01 (Zea mays), 3'ss of exon 1
--------------------------aagttatttgtctgctggaaattt----------tcccatt-------------gattattgctctgt-tactataacta-tgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| | ||| ||| |||||| || |||| || | | | ||| | | ||| | | | | | |||| || | | | | | | |||| ||||||| || || ||||| |||||||| ||||||||||||| || || | ||||| ||||| ||||| ||||||||||| ||||| ||||| |
gtttgctaacatttgctgattgtgttgtaatttctgtacactgcaaatttggatatagagtctcattaagaagaaaaagggagaagtcccctgagtgttctaattggttgattgcctgacaccttcgtttttcatcttctatcttgcatagGTCATTGCTGTGAAGCAACTTGATAGAAATGGTTTTCAAGGAAATCGTGAATTCCTTGTGGAGGTTCTCATGCTAAGTCTCTTGCACCATCCTAATCTGG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G037585_T01 (Zea mays), 3'ss of exon 2
---------------------------------------------------------aagttatttgtctgctggaaattttcccattgattattgctc-----tgttactataactatgcctctttcg--------taatcttcattaatgaaatcattct-cttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
|| || |||| || | | | | ||| | || || ||||| || ||| || || | | || | | | || | |||| |||| |||||||| || || ||||| || ||||| || ||||||||| | || ||| |||| || ||||| |||||||||||||| ||||| | || || |
gtaagcatatctgaaacatgacgcattgacattttgattgtaaagctaaatcctctcaaatttggcttctgagttgaaacattaagtaaaatgttggtgggaaatgctaacataacgattatacttgcgccctggattagccctggatactaacagagttttacttcccagGCTGTTGCTGTGAAGCAACTTGATCGTAATGGCCTCCAAGGAAATAGGGAATTTCTGGTTGAGGTTCTCATGCTCAGTCTCTTACATCACACTAACCTGG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G18610.1 (Arabidopsis thaliana), 3'ss of exon 3
aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
||| || ||||| | || | | | | || | || | |||| |||| ||||| || |||| | || ||||| ||||||||||| ||||| ||||| |||||||| |||||||| | || || ||||||||||| || || |||||||||| |||||||
---------------gtgaagttcgtaaattgaat-ttaatgtttcataatcaagattcgtcttc--taattggatttaata----------ttttgcagATAGTAGCTGTTAAACAGCTTGATCGAAACGGTCTACAAGGAAACAGAGAGTTTCTTGTAGAGGTTCTTATGCTGAGCCTTCTGCATCATCCCAATCTTG
upper sequence: GLYMA15G10360.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0020g01770.t01 (Vitis vinifera), 3'ss of exon 2
aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcc--tctttcgtaatcttca-ttaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
| | ||| | | ||||| | ||| || || | | ||| | || | | ||| | || || || | ||| ||| | || |||||| |||||||| ||||| |||||||||||||| |||||||||||| |||| || |||||||| ||||| ||||| || ||||| ||||| ||||| ||||
-aatcttttatata-tggaatatggattgctgaataatg-ttaatcactgtgtctcatctggtatttattgatttttggttcaatgaattattgtatttgcagGTAGTTGCTGTGAAACAACTTGACCGAAATGGCCTTCAAGGAAATAGAGAATTCTTGGTGGAGGTTCTCATGCTTAGCCTCTTACATCACCCAAACCTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
cattaat putative branch site (score: 3)
tcattctcttc putative PPT
attaatgaaatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagttatttgtctgctggaaattttcccattgattattgctctgttactataactatgcctctttcgtaatcttcattaatgaaatcattctcttcgcagGTGGTTGCTGTAAAACAGCTTGACCGAAATGGTCTTCAAGGAAATCGAGAGTTTTTGGTGGAAGTTCTTATGCTCAGTCTCTTGCATCATCCAAATCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - -ctgctgg
- - - - - - - - - - - tttccca
- - - - - - - - - - - - - - - - - - -tgctctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttcatt
