Sequence
atgc intronic sequence ATGC exonic sequencegtcttatttttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G23190.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 9
gtcttatttttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
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----------------gtaatgagttcttctattgtcacaagtttctacttaaaatatggcttgggaattcatcact-tatgtt--tttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTCACCTATGCAAAAGAGTTGGTTGAACGGATGGGTCTTGGAAAGTCATCCTCAAATGTTGAACCTC
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 9
gtcttatttttgtctaaccaagaaacgctatt-ccataaatgattacaaatacacctccaggctcaatatttac-cacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC---
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-------------gtaat-gagttcttctattgtcacaaatatctacttata-atgt---ggctaggtattaattcatcacttatatttttgcaggagGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTCCTG
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 9
gtcttatttttgtctaaccaagaaacgctatt-ccataaatgattacaaatacacctccaggctcaatatttac-cacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
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-------------gtaat-gagttcttctattgtcacaaatatctacttata-atgt---ggctaggtattaattcatcacttatatttttgcagGAGGACTTTGGAGGTGGTCATCCGGATCCTAACCTTACCTATGCAAAAGAGTTGGTTGAACGCATGGGTCTTGGAAAGTCATCCTCAAATGTTGAGCCTC
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 9
gtcttatttttgt-ctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttg----cagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
|||||||| | | | | || || | | || ||| ||| | | | | || | | || ||| ||||| |||||||||||||| || || || ||||||||||| ||||| || ||| | || || || |||||||| || |||||||| | || ||| || |
gtcttattctcttgttgattaatgccaaggatagctttaaatattctgaatgccagttgtgatttgcctttgatttgtggatgacttgttggatacagGAAGACTTTGGAGGAGGACACCCAGACCCCAATTTGACATATGCAAAAGAGTTGGTTGCTCGTATGGGATTGGGCAAATCCGAACCACAAGATGATCCCC
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 10
-----------------------gtcttattt-ttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
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gtttgactgacttgatggactatttcttgtctgttgtaaaattatcaaactgaataatttcaaaacctaagaat-cttttgttatttctttttttggctgatttca--tgcaaacagGAAGACTTTGGAGGAGGGCATCCAGATCCTAATCTAACCTATGCAAAGGAGTTGGTTGCATGTATGGGATTGGGTAAATCAGATGCTAAAAATGAGCCAC
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S4_12V6.3 (Physcomitrella patens), 3'ss of exon 10
--gtcttatttttgtctaaccaagaaacgctattcca---taaatgattacaaataca---cctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC-
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ttgtgctaacttaattagctgggtagaaacatctccagtgcaggcgaatacttttttagtttctccacgcttctttaataacaaactatttt-atatgcagGAAGACTTCGGTGGAGGTCACCCTGATCCCAATTTGACCTACGCTAAGGAACTCGTGCAAGTTATGGGATTGGGCAAGACTCA-ACCTGACGAGATTCCGG
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 8
gtcttatttttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgattt--gcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
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--------------------------------------------gtttgtgtttttct---ttcttcctgttctatacttcaacgttttctacagGAGGACTTTGGTGGAGGCCATCCGGATCCCAATCTCACGTACGCAAAAGAGCTTGTTTTGCGCATGGGACTGGGGAAGACCGGCCCTCCTGCCGATCCAC
upper sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 8
gtcttatttttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgattt--gcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
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--------------------------------------------gtttgtgtttttct---ttctttctgtgccatacttgaacgttttctacagGAGGACTTTGGCGGAGGCCATCCGGATCCCAATCTCACGTACGCAAAAGAGCTTGTTTTGCGCATGGGACTGGGGAAGACCGGCCCTCCTGCCGATCCACMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124845651|gb|EH930088.1|EH930088EST: AAAGACGCATTATTGAACTGCACTCCCAAG GAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAG
genomic: AAAG-CGCATTATTGAACTGCACTCCCAAGgtcttatttt ... cgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAG
EST:
gi|47831641|gb|CK121325.1|CK121325EST: TCGAAGAACTCGGTGCGCAAGAAAGCGCATTATTGAACTGCACTCCCAAG GAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAG
genomic: TCGAAGAACTCGGTGCGCAAGAAAGCGCATTATTGAACTGCACTCCCAAGgtcttatttt ... cgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgattacaaatacacctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
tcaatattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtcttatttttgtctaaccaagaaacgctattccataaatgattacaaatacacctccaggctcaatatttaccacaatacaacgatttgcagGAGGACTTTGGAGGAGGGCATCCGGATCCCAATTTGACCTATGCTAAGGAGCTTGTGGCACGAATGGGATTAGGTAAATCCGACACTGGAGGTGAACCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG