Sequence
atgc intronic sequence ATGC exonic sequencegtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgagaagtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29320.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g55090.1 (Oryza sativa), 3'ss of exon 10
gtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgagaagtcctttacgcaactctg-agtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
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----------------------------------------------------gtatatttaataggaagcattttcattctatcatgtattggttcacttag------tttttgtcacctgga------ttcacagGTGAAAAGGATCCATGAGTATAAGCGACAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGTGCAAAAGACAGAATAA
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G074158_T01 (Zea mays), 3'ss of exon 10
gtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgagaagtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
| ||| | | | | || || | |||||| | || | | | ||| | | || | | ||| ||| ||| | | || || | || | |||||||| || ||||| || |||||||||||| | |||||||| ||||||||||| |||||||| |||||||| | || |||| |
-----------------------------gcaatgaaaaataactagttt---cttataggtttgctcattcttatcagaaaccatatgctatttgttgattgacttgggatttctcatctggatccctt---agGTGAAAAGGATACATGAATATAAGCGGCAGCTGCTAAATATCCTTGGAATTGTCTACCGCTACAAGAAGATGAAAGAAATGAGCACAGAAGAAAGAGCAA
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G06040.1 (Glycine max), 3'ss of exon 10
gtcagttccaatggatcttggttacttttagattgatgagttgt-ttgcttgggtttttcggtttgaga-agtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
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-------------------------------------cagttatgctacttgtgaattcaatttctacccaatccatcagtattccctatatagttttgctaaactattcactgttggctttatcatttttgtttagGTGAAGAGAATCCATGAATATAAGCGACAATTATTGAACATATTTGGAATTGTTTACCGATACAAGAAGATGAAAGAAATGAGTGCTGCAGAAAGGAAAG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA19G03490.1 (Glycine max), 3'ss of exon 10
gtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgag--aagtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
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------------------------------------caattttgttacgtgtgagttcaatttctacccaatccatttgtact-ccctatatagttttgctaaactattcactgttggctttattatttttgtttagGTGAAGAGAATCCATGAATATAAGCGACAATTAATGAACATATTTGGAATTGTTTACCGATACAAGAAGATGAAAGAAATGAGTGCGGCAGAAAGGGAAG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv14s0108g01560.t01 (Vitis vinifera), 3'ss of exon 10
gtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgagaagtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
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------------------ttgtttcctcaccactccttggc--tttgcttttctacctcattcaaaatacgtttctttataaatctttatggact--gtagattgagttgcttta-------------ttttcagGTGAAGCGTATCCATGAATACAAGCGTCAACTGTTGAACATCTTGGGAATTGTTTATCGCTATAAAAAGATGAAAGAAATGACTGCAGCAGAGAGGAAAG
upper sequence: AT3G29320.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ09932 (Selaginella moellendorffii), 3'ss of exon 9
gtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgagaagtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
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-------------------------------------------------------------------------------------------gtctcaccatgtgaggttctcactaaa---agactatttaacagGTGAAAAGAATCCACGAGTACAAGCGTCAACTGCTAAACATTTTAGGATGCATCTACCGCTACAAAAAGATGAAAGAAATGAGTCCAAAAGAGAGGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
ctttttgc CT-rich tract
attcttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcagttccaatggatcttggttacttttagattgatgagttgtttgcttgggtttttcggtttgagaagtcctttacgcaactctgagtagcttatgtagattcttttctttttgcattgaaaactttttgcagATCAAGCGTATACATGAGTACAAGCGACAACTGCTAAATATCTTGGGAATTGTTTACCGCTACAAAAAGATGAAGGAAATGAGTGCTAGTGAGAGAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA