Sequence
atgc intronic sequence ATGC exonic sequencegttagtgattgtcatttgtcaattattgttttttataatctttttgtggcaatgccacttttggggttgaaattgggttgactttgtaaattactcttcattttcattttcagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
Basic information
species | Arabidopsis thaliana |
transcript | AT5G45160.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G45160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os12g41170.1 (Oryza sativa), 3'ss of exon 2
gttagtgattgtcatttgtcaattattgttttttataatctttttgtggcaatgccacttttggggttgaaattgggttgactttgtaaattactcttcattttcattttcagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
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---------tgaactggatctctcacaggaactcatagtcacactattacattttgatttctggtagggaaataccatga----tatcactgatattatgcctatgtctttagGAGTCAAACTACCAAAGGTATCTGGATAGCACGATGTGTTGGTGTTGAGCCGTGTACTGTTGTGATGGATTTGGAGGGTACTGATGGAAGAGAAAGAGGA
upper sequence: AT5G45160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G052619_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------gttagtgattgtcatttgtcaat---tattgttttttataatctttttgtggcaatgc-cacttttggggttg--aaattgggttgactttgtaa--attactcttc-attttcattttcagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
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gtatgtaacatttgctccccccttgattatctttgtttattcattcatatataaataatttattaactaatttcttgtcatttttttatacccattatcacccctaaccttatcatgaaaacacatgctgctgctattatttatttatgttgatagaaaaattgttgctgttctatttttcttattagGAGTCAAACTACTAAAGGTATCTGGATAGCACGCTGTGTTGGTGTTGAGCCTTGTACTGTTGTATTGGATCTTGAGGGTACCGATGGAAGAGAGAGAGGA
upper sequence: AT5G45160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G13380.2 (Glycine max), 3'ss of exon 2
-------------gttagtgat-tgtcattt--------gtcaatt-attgttttttataatctttttgtggcaatgccacttttggggttgaaattgggttgactttgtaaattactcttcattttcattttcagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
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gtcggtttctgaaattattgagatgttgttttgggcagagaaaactgaatgtctttttgacgttcttggtggcagttatgttttagacttttagttta--ttgaacatgtaattgagtat-catgttg--ttgcagATCGCAAACGACCAAGGGCATTTGGATAGCCAAGTGTGTTGGGATTGAGCCAAGCACAATTGCTATGGATTTAGAGGGTACTGATGGAAGAGAGAGAGGC
upper sequence: AT5G45160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA09G02490.1 (Glycine max), 3'ss of exon 2
gttagtgattgtcatttgtcaattattgttttttata-----atctttttgtggcaatgccacttttg--gg--gttgaaattgggttgactttgt--aaattactcttcattttcatttt----cagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
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gttcggttctgaaattattggactgttgtttggggcagagaaaactgaatgtctttttgacattcttgctggctgttatgttttagtttagtttattgaactcgtaattgagtatcatattgttgcagATCTCAAACGACCAAGGGCATTTGGATAGCCAAGTGTGTTGGGATTGAGCCAAGCACAATTGCTATGGATTTAGAGGGCACTGATGGAAGGGAGAGGGGC
upper sequence: AT5G45160.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0125g00430.t01 (Vitis vinifera), 3'ss of exon 2
----------------------gttagtgattgtcatttgtcaattattgttt-tttataatct-ttttgtggcaatgccacttttggggttgaaattgggttgactttgtaaattactcttcattttcattttcagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
|| || || | | || |||||| ||||| | ||| | || ||| | | | | | | || |||| | | | ||||||||||||||||| || ||||||||||| | |||||||||||||||||||| |||||||| |||||||| ||||| ||||||||||| |||||||||
gttagttttttagtttcttaagctttgtatttttaaagggtgtgggtttgtttgtttatttcttgtttcttttttattttgttttaacattcccgacaatatgagagacatgagatgtaatttctttttactat-agGAGTCAAACAACTAAGGGAATTTGGATGGCAAATTGTGTTGGTATTGAGCCTTTAACAATTGCCATGGATTTAGAGGGCACTGATGGGAGGGAAAGAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttggggttgaaattgggttgactttgtaaattactcttcattttcattttcagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
ggttgac putative branch site (score: 4)
ttactcttcattttca putative PPT
ttcattttcatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgattgtcatttgtcaattattgttttttataatctttttgtggcaatgccacttttggggttgaaattgggttgactttgtaaattactcttcattttcattttcagGAGTCAAACAACTAAAGGTATTTGGATGGCTAGGTGTGTTGGTATTGAGCCTTTCACAATTGCTATGGATTTGGAGGGTACTGATGGGAGAGAAAGAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG