Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaaatgaattcatttctcttatgctatgattcttctttgttttgttggaatgcattgtttttgaaagtggtttgtgatgatgggacagTTGAAGAGCTGTTTTGGGTTCGATACATTTTTCGCTACGGATGTTCGCCGGTTTGGAGATGGAGGAATCTTCATTGGGAACCTGAGAAAACCCATTGATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G17870.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G17870.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA01G45240.1 (Glycine max), 3'ss of exon 1
gtaaaaaaatgaattcatttctcttatgctatgattcttctttgttttgttggaatgcattgtttttgaaagtggtttgtgatgatgggacagTTGAAGAGCTGTTTTGGGTTCGATACATTTTTCGCTACGGATGTTCGCCGGTTTGGAGATGGAGGAATCTTCATTGGGAACCTGAGAAAACCCATTGATG
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---gtcacctcgcctcattccactcccatcactattcatttccactctattctattac-taatttt----atttgtctggcgttatg---cagTTAAAGAGTTGCTTTGGATTTGACACCTTCTTCGCTACCGATGTTCGAAGATTTGGAGATGGAGGCATTTTCATTGGCAATTTGAGGAAACCCATCGATG
upper sequence: AT1G17870.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0088g00320.t01 (Vitis vinifera), 3'ss of exon 1
----gtaaaaaaatgaattcatttctcttatgctatgattcttctttgttttgttggaatgcattgtttt--tgaaagtggt--ttgtgatgatgggacagTTGAAGAGCTGTTTTGGGTTCGATACATTTTTCGCTACGGATGTTCGCCGGTTTGGAGATGGAGGAATCTTCATTGGGAACCTGAGAAAACCCATTGATG
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aaagggtcattgatggtttaatttttgcacttctaattattgtgtgggatgcattcaaatgtattggtttgtctatgatggaaattgtgttcttttt-cagTTAAAGAACTGTTTTGGGTTTGATACATTTTATGCAACTGATGTTCGGAGGTTTGGAGATGGGGGAATTTTTATTGGGAATTTGAGGAGACCCATTGAAG
upper sequence: AT1G17870.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ16045 (Selaginella moellendorffii), 3'ss of exon 1
gtaaaaaaatgaattcatttctcttatgctatgattcttctttgttttgttgg-aatgcattgtttttgaaagtggtttgtgatgatgggacagTTGAAGAGCTGTTTTGGGTTCGATACATTTTTCGCTACGGATGTTCGCCGGTTTGGAGATGGAGGAATCTTCATTGGGAACCTGAGAAAACCCATTGATG
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-----------------------gtatgcgttcctttttttttctctctttggcagttccttgctcttaaatgtgacttt----------gcagTTGAAAAGCTGCTTTGGATACGATACATTCTATGCGACCGATGTTCGCCGCTTTGGAGACGGTGGAATTTACATTGGAAACTTGAGAAAGCCAATCGATG
upper sequence: AT1G17870.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: EFJ16924 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaaaaatgaattcatttctcttatgctatgattcttctttgttttgttggaatgcattgtttttgaaagtggtttgtgatgatgggacagTTGAAGAGCTGTTTTGGGTTCGATACATTTTTCGCTACGGATGTTCGCCGGTTTGGAGATGGAGGAATCTTCATTGGGAACCTGAGAAAACCCATTGATG
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----------------------------gtatgcgttcctttttttttttc----tcttttgctcttaaatgtgacttt----------gcagTTGAAAAGCTGCTTTGGATACGATACATTCTATGCGACCGATGTTCGCCGCTTTGGAGACGGTGGAATTTACATTGGAAACTTGAGAAAGCCCATCGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttgttttgttggaatgcattgtttttgaaagtggtttgtgatgatgggacagTTGAAGAGCTGTTTTGGGTTCGATACATTTTTCGCTACGGATGTTCGCCGGTTTGGAGATGGAGGAATCTTCATTGGGAACCTGAGAAAACCCATTGATG
attgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaaaatgaattcatttctcttatgctatgattcttctttgttttgttggaatgcattgtttttgaaagtggtttgtgatgatgggacagTTGAAGAGCTGTTTTGGGTTCGATACATTTTTCGCTACGGATGTTCGCCGGTTTGGAGATGGAGGAATCTTCATTGGGAACCTGAGAAAACCCATTGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA