Sequence
atgc intronic sequence ATGC exonic sequencegttaatatattattgaaatttgcttaacttttttcctagtgtgtgtgtgtgtgtgaatgaaaatgctcttgctaacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
Basic information
species | Glycine max |
transcript | GLYMA02G47860.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G47860.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G830250_T01 (Zea mays), 3'ss of exon 7
--------------------------gttaatatattattgaaatttgcttaacttttttcctagtgtgtgtgtgtgtgtgaatgaaaatgctcttgctaacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
| | || || | |||||| || | || | | | | ||| | | | | | | ||||||||| || |||||| ||| |||||||||||| ||||||| | ||||||| || ||||| |||||| |||| |||||||||||||| |||||
tgtctatttttagctgaccagtactgtccagtgtactaactactattgcttgtctagccttctgctac-cacttatatctgatttgcttta-tatcgtt--cagTGATGGAGCTGCTGCATTAGCTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAAAGGATATGCTGATGCAGCTCAA
upper sequence: GLYMA02G47860.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 9
---gttaatatattattgaaa---tttgcttaacttttttcctagtgtg---tgtgtg----tgtgtga------atgaaaatgctcttgct---aacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
|| || | | ||| | || | | |||| | || ||||| | || | || || | | || | ||||||||| || |||||| ||||||| |||||||| ||||||| | ||||||| |||||||| |||||| |||| || ||||||||||| |||||
tgtgtctatttttagctgacaagtactgtccggtgtactgcctactatggcttgtgtagccttctgcaaccagtcatctaatttgttttatatggatcagTGATGGAGCTGCTGCATTAGTTTTAGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTTCAAGTCCTTGCAAGGATCAAAGGTTATGCTGATGCAGCTCAA
upper sequence: GLYMA02G47860.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G085474_T04 (Zea mays), 3'ss of exon 9
-----------------gttaatatattattgaaatttgcttaacttttttcctagtgtgtgtgtgtgtgtgaatg---aaaatgctcttgct---aacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
| | || | | | | || | | || |||| | | || | |||| || | ||||||||| || |||||| |||||||||||||||| ||||||| | ||||||| || ||||| |||||| |||| |||||||| ||||| |||||
tgctattttttccattggctggtaccgt-tcagtgtgtactgcctactactgctggtgtagctacaatcggtcatatctgatttgcttttatatggatcagTGATGGGGCGGCTGCATTAGTTTTGGTGAGTGGGCAGAAGGCTCAAGAGCTTGGCCTGCAAGTCCTTGCAAGGATCAGAGGATATGCAGATGCGGCTCAA
upper sequence: GLYMA02G47860.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv12s0057g01200.t01 (Vitis vinifera), 3'ss of exon 9
----------------gttaat-atattattgaaatttgc---ttaacttttttcctagt-gtgtgtgt-gtgtgtgaatgaaaatgctcttgctaacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
| ||| || ||| || | || || || | | | || | ||| | | || | || || ||||||||||||| ||||| |||||||||| ||||||||||||||||| | |||||||| ||| ||||| || || | ||||| |||||||||||||||
aattaaaattgtaattgaaaatgattccatttaagtatgtgggttgacatccattttggttatctgtcttatactgaaaagtgaaattgctcatcgacagTGATGGTGCTGCTGCTTTAGTTTTGGTAAGTGGAGAGAAGGCACTTCAACTTGGGCTGTCAGTCATTGCTAAGATTGCAGGATACGCTGATGCTGCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaacttttttcctagtgtgtgtgtgtgtgtgaatgaaaatgctcttgctaacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
gcttaac putative branch site (score: 3)
ctcttgct putative PPT
aatgaaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaatatattattgaaatttgcttaacttttttcctagtgtgtgtgtgtgtgtgaatgaaaatgctcttgctaacagTGATGGTGCCGCTGCACTAGTTTTGGTGAGTGGAGAGAAGGCACTGAAGCTTGGGCTTCAAGTTATTGCAAAAATCACTGGATATGCTGATGCTGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT