Sequence
atgc intronic sequence ATGC exonic sequencegtaagcctcctctttttagtttacattataggaaacagaagatgaaatctttgcttctctgtcaatcctttttctcatataactcatcttgccaataaggcaataaccaaatgatctaatttgatttcagGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G71830.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 7
gtaagcctcctctttttagtttacattataggaaacagaagatgaaatctttgcttctctgtcaatcctttttctcatataactcatcttgccaataaggcaataaccaaatg-atctaatttgatttcagGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG---
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-----gtgattctctatagttttaattctgttacatttgtgata---------ctgcttgggatatgcatatgcataaatgatgcagacaggggatttgaca-tattcgggtggaattaattctattccatcagGTGACTCCAAAACTGGAGCAATTGCTGGAGGTGTTGCTGCAGCTGCTGCATTGCTGTTTGCGGTTCCGGCAATTGGATTTGCATGGTGGCGGCGGCGTAA
upper sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G115420_T01 (Zea mays), 3'ss of exon 7
gtaagcctcctctttttagtttacattataggaaacagaagatgaaatctttgcttctctgtcaatcctttttctcata-taactcatcttgccaataaggcaataaccaaatgatctaatttgatttcagGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG---
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-------------------------------------gtaggttttgaatctacttttattttcattaatacactaaaactttagcattttggatgacacgtacttcctggat--ttatgtctactattagGTGCTTCTAGCA---CTGGAGCAATAGCTGGAGGTGTTGCTGCTGGTGCAGCATTGGTGTTTGCTGTTCCTGCAATTGCATTTGCAATGTGGCGCCGTCGTAA
upper sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G384439_T02 (Zea mays), 3'ss of exon 7
gtaagcctcctctttttagtttacattataggaaacagaagatgaaatctttgcttctctgtcaatcct-ttttctcatataactcatcttgccaataaggca-ataaccaaatgatcta-atttgatttc-------agGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG
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-------------------------------------aataactaccttcttttttttgtccctaccctgcattagtatggcagtaattaaggctatggaacatatggctttgttactgacatcttattttttgcagGAAGTAGCTCTTCCAGTACTGGAGCAATTGCTGGTGGAGTGGCTGCTGGTGCAGCCTTGCTATTTGCTATTCCTGCAATTAGTTTTGCCTATTGGCGGCG---
upper sequence: AT1G71830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv07s0031g01410.t01 (Vitis vinifera), 3'ss of exon 7
gtaagcctcctctttttagtttacattataggaaacagaagatgaaatctttgcttc--tctgtcaatcctttttctcatataactcatcttgccaataaggcaataaccaaatgatctaatttgatttcagGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG
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-------------------------------gtgattggataattgctttttgttgaaatccaaaatttctattattttcagatctgcactagaggattaaattatttgtttcttttcaaatgtcatt-cagGAGGAAATAGTGCCACAGGAGCAATTGCTGGAGGAGTGGCTGCTGGTGCTGCTTTACTGTTTGCTGCACCAGCAATTGGTTTTGCATGGTGGCGGCGGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catataactcatcttgccaataaggcaataaccaaatgatctaatttgatttcagGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG
aaatgatctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcctcctctttttagtttacattataggaaacagaagatgaaatctttgcttctctgtcaatcctttttctcatataactcatcttgccaataaggcaataaccaaatgatctaatttgatttcagGTGGGTATGGTATAACTGGAGCAATAGCTGGTGGAGTTGCTGCAGGTGCTGCTTTGCTCTTTGCTGCTCCTGCAATAGCCTTTGCTTGGTGGCGACGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG