Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaaagtttcacctattcatgcattatatactattttcctagagtatccaattatctgacatcacattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57610.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os02g54510.2 (Oryza sativa), 3'ss of exon 5
gtaaaaaagtttcacctattcatgcattatatactattttcctagagtatccaattatctgacatc-acattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
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--------gtattacttgtttaatcaaagaacactatgattcttttattctcaaatatccaaattctaaattaaagcaactgcacagGACAATTGATCGCCGTAAAAGAGTTATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCATGGGAAGAATATAGTTCATTTTGATCTAAAGTGT
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 3
gtaaaaaagtttcacctattcatgcattatatactattttcctagagtatccaattatctgacatcacattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
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------gcactacattttctaaagcaagaaataagaatatatttggtcttctatttctcctttatcaaaataaagcacttgtgcagGACAATAGATCGCCGGAAGAGAGTAATATTAGCCATGGATGCTGCATTTGGCATGGAATATTTGCACGGGAAGAATATAGTCCATTTTGACCTGAAGTGT
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 4
gtaaaaaagtttcacctattcatgcattatatactattt--tcctagagtatccaattatctgacatcacattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
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gtactatatattga---atccaagaaata-agaatatttgatcttttatttctcctgtatcgaactctaaattaaagcgcttgtgcagGACAATTGATCGCCGGAAGAGAGTAATATTAGCCATGGATGCTGCATTTGGCATGGAGTATTTGCATGGGAAGAATATAGTCCATTTTGACCTGAAATGT
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G01190.1 (Glycine max), 3'ss of exon 7
----------------------------------------------gtaaaaaagt-ttcacctattcatgcatt-atat-actattttcctagagtatccaattatctgacatcacattggttg-----actcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
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gtaacttgatgcatgcatgggcttatatttcatcaatatttaatatgttttaaggcactcaaatgtgcagccttccatatgaaaaccctcatggactggtgatgtattatttatgctgtttattctgagcaatttaacagAACAATAGATCGTCGTAAGAGGCTCATTATAGCCATGGATGCTGCATTTGGGATGGAGTATTTGCATGGAAAAAACATTGTTCATTTTGATTTGAAATGT
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G07320.1 (Glycine max), 3'ss of exon 10
---------------------------------------------------------gtaaaaaagt-ttcacctattcatgcattatatactatt--ttcctagagtatccaattatctgacatcacattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
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gtaatttgatgcatgcatgggcttatatttcatcaatatttaatagtatgctttaaggcactgaaatgtgcagccttccatctgaaagccctcatggactgttgatgtatttatttatgctgt-ttattctgagcaatttaac-agAACAATAGATCGTCGTAAGAGGCTCATTATAGCCATGGATGCTGCATTTGGGATGGAGTATTTGCATGGAAAAAACATTGTGCATTTTGATTTGAAATGT
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0052g01480.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------------gtaaaaaagtttcacctattcatgc--attatatactattttccta-gagtatccaattatctg----acatcacattggttgactcctc--cagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
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gtaattgttttgatggtggtttactgaattgcagtttatgagtccttttaactttcttctgttttaggatgtaggctataaagcatatacttagaagtgctcattttttgctgaaaagaaatgaaaaatttatttcctgtggaatgtgacaattttatgctattgaacagGACAATAGATCGTCGGAAGAGACGCATCATAGCTATGGATGCTTCATTTGGAATGGAGTATTTACATGGCAAGAATATTGTACATTTTGACTTAAAATGT
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ30928 (Selaginella moellendorffii), 3'ss of exon 2
gtaaaaaagtttcacctattcatgcattatatactattttcctagagtatccaattatctgacatcacattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
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----------------------------gtacgtgaactcaaaagaggatg-gactgtatcggctaac-ttgccagatttc---agAACCATTGATCGTCGGAAGCGACTGTTGATAGCAACAGACGCTGCTTTTGGGATGGAGTATCTACACGGAAAGAACATCGTTCATTTCGACCTGAAGTGCMapped 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|124966868|gb|EL040942.1|EL040942EST: GAGTTCATGGTTAACGGATCTTTGAAACAGTTCTTGCAGAAGAAGGATAG AACTATTGATCGTCGCAAAAGACTCA
genomic: GAGTTCATGGTTAACGGATCTTTGAAACAGTTCTTGCAGAAGAAGGATAGgtaaaaaagt ... actcctccagAACTATTGATCGTCGCAAAAGACTCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tactattttcctagagtatccaattatctgacatcacattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
ctcctcc CT-rich tract
aattatct 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
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gtaaaaaagtttcacctattcatgcattatatactattttcctagagtatccaattatctgacatcacattggttgactcctccagAACTATTGATCGTCGCAAAAGACTCATCATAGCCATGGATACTGCATTTGGGATGGAGTATTTGCACGGAAAGAACATTGTTCATTTCGATTTGAAGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG