Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttaatctgcctttctttcttttgcaatagcattataaagctcatttattaatattaatctgttaatgctttctgattaacagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17940.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA10G31710.1 (Glycine max), 3'ss of exon 12
-----------------------------------gtgagtttaat-ctgcctttctttcttttgcaat--agcattataaagctcatttattaatattaatctgt-taatgctttc--tgatta--acagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
| | || | | || | | ||| ||| | | ||| | | | | ||| | ||| | || | || | ||| |||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||||| ||||||||||| | || | || | | ||| |
gtaaacattagtgcattagtaaaatgttttaaaatatcatttcattgttgataatgatccttgcttaatgaaaagcaaagaagtagaatgactgataaaatcatgtgttttgttgtcaacgtttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAACTTCCGCAGATGGATCCCTCTTGGAGAACAGAAAAT
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA20G35900.1 (Glycine max), 3'ss of exon 12
-----------------------------------gtgagttta-atctgcctttctttcttttgcaat--agcattataaagctcatttattaatattaatctgt-taatgctttc--tgatta--acagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
| | || | | || | ||||| || | | | ||| | | | | ||| | ||| | || | || | ||| |||||||||||||||||||||||||| | |||||||| || ||||| |||||||||||||| ||||| ||||| | | || | || | | ||| |
gtaagcattagtgcattagtaaattgttttaaaatatcatttcatagttgataatgattcttgcttaacgaaaagtaaagaagttgaaggactgataaaatcatgtgttttgttgtcaacgcttattacagAATCATGGAGACAGCACCAACATTGCCTGATTTTGCCTTGGCTTTGAAACCAGATGAATATCAGCTTCCTCAGGTGGATCCCTCTTGGAGAACAGAAAAT
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA09G29110.1 (Glycine max), 3'ss of exon 12
--------------------------------------gtgagtttaatctgcctttctttcttttgcaatagcattataaagctcatttattaatattaatctgttaatgctttctgattaacagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
|| || | ||||| | || || | ||| | | || | || || | || | | ||| | |||| ||||||||||||||||||||| | |||||||| | ||||| |||||||||||||| ||||||||||| | | || | || | | |||
gtaaactttccaaaatgcacgaataacttgttacttaactgtaattgcttaattattcttggctaatgaaaagtagtatgatgaccaacaa--aaccatattgtgcttttctttttattattacagGATCATGGAGACAGCACCAACATTGCCTGATTTTTCATTGGCCTTGAAACCAGATGAATATCAACTTCCTCAAGTGGACTCATCTTGGAGAACAGAGAAC
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA16G33650.1 (Glycine max), 3'ss of exon 10
-------------------------------------gtgagtttaatctgcctttctttcttttgcaatagcattataaagctcatttattaatattaatctgttaatgctttctgat-taacagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
|| || | ||||| | | || | ||| | | || | || || | ||| | |||| | | | |||| ||||||||||||||||||||| | |||||||| | ||||| |||||||||||||| ||||||||||| | | || | || | | |||
gtaaactttccaaagagcacgagtaacttgttactaactgtaattgcttaattattcttggctagtgagaagtagtatgatgaccaacaa--aaccatattttgtgttttctttttattattacagGATCATGGAGACAGCACCAACATTGCCTGATTTTTCATTGGCCTTGAAACCAGATGAATATCAACTTCCTCAAGTGGACTCATCTTGGAGAACAGAGAAC
upper sequence: AT1G17940.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv16s0039g00390.t01 (Vitis vinifera), 3'ss of exon 13
---------------------gtgagtttaatc---tgcctttctttcttt--tgcaatagcattataaagctcatttattaatattaatctgt------taatgct------ttctgattaacagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
| |||||| ||||| | | || || ||| || || | | || || | ||||| | || || | ||| | |||||||||||||||||||||| ||| |||||||| |||||||| ||||||| ||||| || |||||||| | | || |||| | | || |
gtaagtctttctttggtgttttggcgtttaactctatgcctgttggccattactggaatgaatgaatgaaatgaagctgg-aaaatcattctgtgatgagtgatactggaaaatcttgactg-cagAATCATGGAGACAGCACCACAACTGCCTGATTTTGCTTTGGCCCTGAAACCCGATGATTACCAACTTCCTCCAGTGGACCCTTCTTGGAACGACAACATA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcattataaagctcatttattaatattaatctgttaatgctttctgattaacagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
tgctttct CT-rich tract
tataaagctcatttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttaatctgcctttctttcttttgcaatagcattataaagctcatttattaatattaatctgttaatgctttctgattaacagAATCATGGAGACAGCACCAACACTTCCTGATTTCGCTTTGGCATTGAAACCAGATGAGTATCAACTTCCACTCGCCGAAGCTTCGTAGTCTGAAGATGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG