Sequence
atgc intronic sequence ATGC exonic sequencegtggttccagtcgaagatatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63640.2 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63640.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 15
gtggttccagtcgaagatatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttct-gtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG
| || | | ||| || | | || || ||| ||||||| | || | | | | | | ||||||| ||||||| ||| | ||||||||||| || ||| |||||||||| | || || ||||||||||| ||||||| ||||| |||| | |||||| || || ||||||||
---------------------------------------------------------------------------------acgtgtcattatatttagacatagctttgtttaccattcatttacttttacttgttttgaaggaaaaacataccaagtattgtttccttgacttgcacacACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATTCTGTGAATTCAATGGCAGATGTCCTCGAGTTGATGAAT-----
upper sequence: AT1G63640.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 16
gtggttccagtcgaagatatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgct-attaggttttactaatgttct-gtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG
|| | | ||||| | | ||| |||||| | | | || || | | ||||| | ||| ||||||| | || | | | | | | ||||||| ||||||| ||| | ||||||||||| || ||| |||||||||| | || || ||||||||||| |||||||
-----------------------------------tacttcatgcatctttattttgtatcatgtatgacagtgcat--------gtcattatatttaggcat-agcattgtttaccattcatttacttttacttgttttgaagGAAAAACATACCAAGTATTGTTTCCTTGACTTGCACACACTTGGGATTTGGAATACTGCCCAACCAAATGGGTTGGCTGTTCCTGATGCAAGTATGCATT-------------------------------------------
upper sequence: AT1G63640.2 (Arabidopsis thaliana), 3'ss of exon 15
lower sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 16
gtggttccagtcgaagatatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG---------------------------------
||| || ||||| |||||| | || | | | |||||||||| ||| | |||||||||| ||| | ||||||||| |||| |||||||||||||||||||| ||| | |||||| | ||| || || ||| | |||||||||||
-------------------------------------------------------------------------------------------------------------------aaactactactttttaacttgcttctgtcatgaaatttttttgta---ccctttaacttgcacacacttgggatttggagtaccactcaaccaaatggtttagCTGTCCCTGATGCAAGCATGCACCCTGTTAAATCAACCGCAGACGTACTGGAATTAATGAATATTGGATTAATGAATAGGGCTGTAGGAGCCACTGCGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG
ttcaatacaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtggttccagtcgaagatatccttttctaatctaatatagtgactaaacattttttggagtaggtacactcgtgcatttatatttgcgaccccacagagaaattggtgtggtttagtgctattaggttttactaatgttctgtggttgcgttcaatacaaaatttccttaacttgcatacattagGGATTTGGAACACCGCCTTACCAAATGGGCTAGCAGTCCCTGATGCAAGCATGCATTGTGTGAGATCAACAGAAGATGTTCTTGAACTGATGAATATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG