Sequence
atgc intronic sequence ATGC exonic sequence...taaactggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagattcatatatgggtctaaataaagtttcaaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G27460.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM5G862959_T04 (Zea mays), 3'ss of exon 6
-taaactggtagatagccgttatgacgcagttatggtaaatatgttgctctt--ccatagattcatatatgggtctaaataaagtttcaaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG
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attaccatgtacatgcacattttcgtgtgcctgttactgttgccttatatgtgaccatcatcctgtaagtatcactcatttaatattgatgcacgt---gcagGTATGAAGTACTTGATGAAGAACCAGGTGATGACGAAGAGAGCACTCAAAA---
upper sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA16G07460.1 (Glycine max), 3'ss of exon 5
taaactggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagattcatatatgggtctaaataaagtttc--aaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG
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tgtaatcattgacagaaagaatagtac--ccattatgacattgatcttttgtaattgtccttttcattattttatttgttctcctgtaacatgattttacagATTTGAAGTACTGGATGAGGAACCAGGCGATGATGAAGAAAGCAGTGGCCAAAG
upper sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G08050.1 (Glycine max), 3'ss of exon 6
--taa--actggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagattcatatatgggtctaaataaagtttcaaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG
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tgtaatcattgacagaaaga-gtagtatccattttgacattaatcttttgtaattgtccttgtcattattttatttgttctcctgtgaca---tgatttgacagATTTGAAGTACTAGATGAGGAACCAGGTGATGATGAAGAAAGCAGTGGCCAAAG
upper sequence: AT3G27460.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0066g00210.t01 (Vitis vinifera), 3'ss of exon 6
taaactggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagat-tcatatatgggtc-taaataaagtttcaa--acttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG
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--aacttttttataacagt-gcgat-tgattgtgccctttaataaaattcagcatacatgccttgtattgttcataaatattgatggaacaactatatatgcagATTTGAAGTACTTGATGAGGAACCTGGTGATGATGAAGAGAGTAGTGGCCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gctcttccatagattcatatatgggtctaaataaagtttcaaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG
gtctaaa putative branch site (score: 3)
cttttttcac putative PPT
taaataaagtttcaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaactggtagatagccgttatgacgcagttatggtaaatatgttgctcttccatagattcatatatgggtctaaataaagtttcaaacttttttcacagAGTTGAAGTACTTGATGAAGAACCAGGAGATGATGAAGAAGGAGGTGGCCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact