Sequence
atgc intronic sequence ATGC exonic sequencegtacaaattttcttgtgtaaatatctgatatatgtcttcgaaatctctctcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G22780.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G700148_T01 (Zea mays), 3'ss of exon 7
gtacaaattttcttgtgtaaatatctgatatatgtcttcgaaatctctctcatggca----tttcatggaaat--ttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
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gtactaccttttcttttaacttttctagtgcacctgtacaaaaatgtgtggactgcaatgattttgttgttgtccttcagGTTTTACAGCGTATTTTGATGGGTACTGATGTTGTTAAAAATGTTAACAAGAACAATGCCTCACATGCTGTTCTCTTTGAAGCTCTTGCTCTG
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G05410.1 (Glycine max), 3'ss of exon 7
-------gta-caaattttcttgtgtaaatatctgatatatgtcttcgaaatctctctcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
|| |||||| | | ||| | | | || | |||| | | | || || | |||||||||| | || | ||| ||||||| || |||||||| ||||||||||| ||||| ||||| || |||||||| || ||||||||||| | |||
gtttgtaatatcaaattgacacatccaaaaaaaaaaaa-atagttaacaaattttagtga--gccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGGACTGATGTTGTAAAAAATGTGAACAAAAATAATGCATCCCATGCCGTTCTTTTTGAAGCTCTTGCTCTG
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA12G30520.1 (Glycine max), 3'ss of exon 7
gtacaaattttcttgtgtaaatatctgatatatgtcttcg---aaatctctctcatggcatttcatggaa-atttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
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gtttgtaatatcaaattgacacatccaaaaactttctttagttaacaaattttagtgagccttgattaatcatttcagGTCTTACAAAGGATACTGATGGGAACTGATGTTGTGAAAAATGTGAACAAAAATAATGCATCCCATGCTGTTCTTTTTGAAGCCCTTGCTCTG
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv06s0061g01170.t01 (Vitis vinifera), 3'ss of exon 7
gtacaaattttcttgtgtaaatatctgatatatgtcttcgaaatct----ctctcatggcatttcatggaaa--tttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
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gtactccatttctca-gcgaatatatttcaattctcatcagattttgtaattctaatgaaatctgttgggtggttttcagGTTCTACAACGGATATTAATGGGAACTGATGTTGTGAAAAACGTGAACAAGAACAATGCCTCACATGCTGTTCTGTTTGAAGCCCTTGCTCTT
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S171_160V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------gtacaaattt-tcttgtgtaaatatctgatata----tgtcttcgaaatctctc----tcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
||| | ||| | || || | | || | | || | ||| || ||| ||| | | | ||||| || || ||| ||| || | ||||||||||||||||| | |||||||||||||| |||||||| || || ||||| || || || ||
ctctgcgtcacgttttgggtagaggtttatgttagttacagtttaaatgtgactgcgcctctgtaattccttaggatcacaaatttttcttgctgtg-cagGTTCTACAAACAATCTTGTTGCGTACAGATGTTGTGAAAAACATTAATAAAAACAATGCATCTCATGCTGTTCTCTTTGAGGCACTTTCTTTG
upper sequence: AT5G22780.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S507_6V6.1 (Physcomitrella patens), 3'ss of exon 7
--------------------------gtacaaattttcttgtgtaaatatctgatatatgtcttcgaaatctctctcatggcatttcatggaaattt-cagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
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cactatttacatccaaatgtattgaattactgaggatcctattgatgtttcc-atacttatccttttatccttttctattgcgacgtgttacgttttgtagACTTTGCAGCGCATTTTGTTGGGAACTGATGTTGTAAAGAATGTCAATAAAAACAATGCCTCGCATGCGGTACTCTTTGAAGCACTCGCTCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatatctgatatatgtcttcgaaatctctctcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
atctgat putative branch site (score: 4)
tgatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaattttcttgtgtaaatatctgatatatgtcttcgaaatctctctcatggcatttcatggaaatttcagGTCCTTCAGCGAATATTGATGGGCACAGATGTTGTGAAAAATGTGAATAAAAACAATGCGTCTCATGCCGTGCTGTTTGAAGCTCTCTCCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC