Sequence
atgc intronic sequence ATGC exonic sequencegtaagttaaagaaattagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G22950.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 5
gtaagttaaag--aaattagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
||| ||| ||||| | || | | || || | ||| || || | | | |||| | | | | ||||| || || | | |||| ||||||||||| |||||||| |||||||| |||||||||||||||||||||||||| ||||| || || | || || |||||||| ||| | || ||
-taaactaacataaaatttattaatgtggaaaatcaagaatttcctagtttgtttca-taacttactcttgactgttctttgtacttctgcttggcatt-------cagGGAGTGCTCCTCTTACTGCTGTCCAACTGCTCTGGGTTAACATGATCATGGACACACTAGGAGCACTGGCATTGGCAACTGAACCTCCAAACGATGAACT
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
----------------------------gtaagttaaagaa-----attagctgattctgtttttattcaaattttcattt-ttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
|| || | | | || ||| | | | | | | |||| ||| ||| | || ||||| |||| | | || | | || || | | |||| ||||||||||| |||||||| ||| |||| ||||| |||||||||||||| ||||| || || || || | || |||||||| || ||||| || ||
gtacatccgatatcctgtatatgagttcgtggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatat-gtctcattgttcgcattcatgctgattgctgatt-------cagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
gtaagttaaagaaattagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
| |||| | | | || || | | || || | ||| | || | || || || | | || |||| || ||||| || || || || || ||||| ||||| ||||||||||||||||| || ||||| || || || || || || ||||||||| |||||||
-------------gtaagcttccaaagaactggtgaaagca---atctgtcgccatgcatgcttgcttgat--ctgctgctgctgctgcttgtgttgtggatc-cagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G118919_T01 (Zea mays), 3'ss of exon 3
gtaagttaaagaaatt-----agctgattctgtttttattcaaat--tttcatttt---tttacaattata----ttgtcttc-gtttctatctttactttt---gtttctaaattaattca-cagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
|||| ||| || | |||| | | | || | | || || | | | | ||| ||| ||| || | || ||| | | | | ||||| |||| || || || || ||||| || || ||||| ||||| ||||||||||||||||| || |||||||| || | || || || || || ||| |||||||
gtaaaaaaaaaaacctcacgctgctgcgttcatctgtaggtgactgattccagtctgaatctgaaataatagacattgactggagcccgtaaacaaactcataaaatgtgcttgtcgattcatcagGGAGCGCGCCCCTGACTGCGGTGCAGCTGCTCTGGGTGAACATGATCATGGACACGCTGGGAGCTCTGGCGTTGGCCACGGAGCCCCCCAACGACGAGCT
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
---------------------------------------------------gtaagt--taaagaaattagctgattctgtttttattcaaattttcat------ttttttacaattatattgtcttcgtttctatct--tta-----cttttgtttctaaattaatt-------cacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
||| || ||| | || || |||||| | | | | ||| || | | || | | | | || |||| ||| ||| ||| || | || || ||| |||||| ||| || || || ||||||||||| | ||||| |||||||| ||||||||||| ||||| |||||||| ||||| |||||||| || | || |
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
-----------------------gtaagttaaagaaattagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
|| ||| ||| ||| | |||| ||| | | ||||| | | | || | | || | | | | || | | | | | |||||| ||| || || || ||||||||||| | ||||| |||||||| ||||||||||| ||||| |||||||| ||||| |||||||| || | || |
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgt--tttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 4
gtaagttaaagaaat-tagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatct---ttacttttgtttctaaattaattcaca-------gGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
||||| | || | ||| ||| ||| | | || |||| | ||| | || | | ||||| || || |||| || || || |||| | |||| |||||| || || |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| |||| || || || || | | || |
gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgtcaaataaacttcttcttttttctccctacattttttttattccttttttttttcaaacacttaagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACCGAGCCACCTACTGATGACTT
upper sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttaaagaaat-tagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatct---ttacttttgtttctaaattaattca-------cagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
||||| | || | ||| ||| ||| | | || |||| | ||| | || | | ||||| || || |||| || || || |||| |||||| |||||| || || |||||||| || || ||||| |||||||||||||| ||||| ||||||||||| |||| || || || || | | || |
gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgtcaaataaacttcttcttttttctccctacattttttttattccttttttttttcaaacacttcagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACTGAGCCACCTACTGATGACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
tatctttacttttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttaaagaaattagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT