Sequence
atgc intronic sequence ATGC exonic sequencegtgtttttccttgccatgtattacaaagacatttatatatttcctgttggtgatttcactatgttgaatcttaacagcaagctgtttatgcagGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAAAATCAATGTGGAGAAGGCCGTTAAGTACATTGTGAGCTGCAAAAACCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G12210.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G11710.1 (Glycine max), 3'ss of exon 5
gtgtttttccttgccatgtattacaaagacatttatatatttcctgttggtgatttcactatgttgaatcttaacagcaagctgtttatgc-agGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAAAATCAATGTGGAGAAGGCCGTTAAGTACATTGTGAGCTGCAAAAACCTG
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gtatttttcttaagatccttttttgttattgattatgtaagagcttactgtatttttaac---taaaatc----cactgaattatttgtcttagGTTCTCATATATTGCTATTTGTTGTCTATCAATATTACATTGCTTGGATAAAATCAATGTGGAGAAGGCAGTGAAGTACATTATAAGTTGCAAAAATATG
upper sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G28630.1 (Glycine max), 3'ss of exon 4
gtgtttttccttgccatgtattacaaagacatttatatatttcctgttggtgatttcactatgttgaatcttaacagcaagctgtttatgc-agGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAAAATCAATGTGGAGAAGGCCGTTAAGTACATTGTGAGCTGCAAAAACCTG----------------------------------------------------------------------------
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gtatttttcttaagattcttttttattattgatcatgtaagagcttactgtatttttaac---taaaatc----cactgaattatttgtcctaggttctcatatattgctatttgttgtctatcaatattacatcgcttggataaaatcaatgtggagaaggctgtgaagTACATTATTTTTTTTTTCTTCGTACCCCATTGCCCAGAGGCTCTTCGCTATGCGAAGGTATGGGGGAGGGATGTTGCACGCAGCCTTACCCTTGCATATG
upper sequence: AT5G12210.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0134g00150.t01 (Vitis vinifera), 3'ss of exon 5
gtgtttttccttgccatgtattacaaagac----atttatatatttcctgttggtgatttcactatgtt----gaatct-taacagcaagctgtttatgcagGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAAAATCAATGTGGAGAAGGCCGTTAAGTACATTGTGAGCTGCAAAAACCTG
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gtattcttttccacaagatccttcattattctgggttcatgattcctttgaagtaagtttccatatgttctggaagtctctgactatagaatttttttgtagGTTCTCTTATATTGCTATATGTTGTCTCTCTCTATTGCAATGTCTGGACAAAATCAATGTGGAGAAGGCTGTGAACTACATCGTGAGTTGCAAAAATCTGMapped 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|19874896|gb|AU235727.1|AU235727EST: AATGAAGATGGATCCTTCTNAGGAGATATGTGGGGAGAAATAGATACNAG GTTTTCGTACATAGCTATTTGCTGNCTCTCAATATTGAAATGTCTTGACAA
genomic: AATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAGgtgtttttcc ... gtttatgcagGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAA
EST:
gi|124728136|gb|EH819538.1|EH819538EST: AATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAG GTTTTCGTACATAGCTATTTGCTGTCTCTCAATATT
genomic: AATGAAGATGGATCCTTCTCAGGAGATATGTGGGGAGAAATAGATACGAGgtgtttttcc ... gtttatgcagGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttcctgttggtgatttcactatgttgaatcttaacagcaagctgtttatgcagGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAAAATCAATGTGGAGAAGGCCGTTAAGTACATTGTGAGCTGCAAAAACCTG
tcttaac putative branch site (score: 2)
aatcttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttttccttgccatgtattacaaagacatttatatatttcctgttggtgatttcactatgttgaatcttaacagcaagctgtttatgcagGTTTTCGTACATAGCTATTTGCTGTCTCTCAATATTGAAATGTCTTGACAAAATCAATGTGGAGAAGGCCGTTAAGTACATTGTGAGCTGCAAAAACCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC