Sequence
atgc intronic sequence ATGC exonic sequencegtaataaaataagctttaaactaactatcttaaacaaaacgcttcttgattctcaatattctgttttcttgatttcttggatctttggttcttgattcttgaaacctgaatcttttatttttggcttaattttgttgtattatacgtctatggttgttggcagGTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAACAAGGATTCATGGAAGCAATTTCAATTCCTCAAATTGAGTGTTTCCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G38530.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G38530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G07130.1 (Glycine max), 3'ss of exon 4
gtaataaaataagctttaaactaactatcttaaacaaaacgcttcttgattctcaatattctgttttcttgatttcttggatctttggttcttgattcttgaaacctgaatcttttatttttggcttaattttgttgtattatacgtctatggttgttggcagGTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAACAAGGATTCATGGAAGCAATTTCAATTCCTCAAATTGAGTGTTTCCAAG
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-----------------------------------------------------aagaaatct---tcctaggtttcc---attttcgtttatgaaattgtatgttcactatcacatgtactatg-tgaatctt--tctatta-acatgtttgtttctttgtagGGGGTTTGCGTTACCACGGTATGGCACCATTGATCTCACATGTTTATGACTTGGGTTTAATGGAAGCAATTGCAATTCCACAAACAGAATGTTTTCAAG
upper sequence: AT5G38530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G05630.1 (Glycine max), 3'ss of exon 1
gtaataaaataagctttaaactaactatcttaaacaaaacgcttcttgattctcaatattctgttttcttgatttcttggatctttggttcttgattcttgaaacctgaatcttttatttttggcttaattttgttgtattatacgtctatggttgttggcagGTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAACAAGGATTCATGGAAGCAATTTCAATTCCTCAAATTGAGTGTTTCCAAG
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--------------------------------------------------------gaacaaatcaacataggtttcc--atttatggttatgaaat--tgcacgttcactatcacatgtactagtgaatctt--tgtatta-acatgtttgcatatttttagGGGGTTTGCGTTACCACGGTATGGCACCATTGATCTCACATGTTTTTGACTTGGGTTTAATGGAAGCAATTGCAATTCCACAAACAGAATGCTTAG---
upper sequence: AT5G38530.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv14s0083g00460.t01 (Vitis vinifera), 3'ss of exon 4
gtaataaaataagctttaaactaactatcttaaacaaaacgcttcttgattctcaatattctgttttcttgatttcttggatctttggttcttgattcttgaaacctgaatcttt-tatttttggcttaattttgttgtattatacgtctatggttgttggcagGTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAACAAGGATTCATGGAAGCAATTTCAATTCCTCAAATTGAGTGTTTCCAAG
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------------------------------------------------------------------------------------gtaatactttgttgctataaggagcttctatatatgtgaagttttgcttctttctgaagaatgtcccctacttt--acagGCGGTTTGCGTTACCATGGTATGGCACCATTGCTTTCACATGTCTATGAACTGGGTTTCATGGAAGCAATCTCAATTCCTCAGATTGAATGCTTTCAAGMapped 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|116461702|gb|EG504294.1|EG504294EST: GAAGATGCATACTTTGGGACATGACTTCATTCCTGATCCTATCCATGACG GTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAAC
genomic: GAAGATGCATACTTTGGGACATGACTTCATTCCTGATCCTATCCATGCCGgtaataaaat ... ttgttggcagGTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatcttttatttttggcttaattttgttgtattatacgtctatggttgttggcagGTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAACAAGGATTCATGGAAGCAATTTCAATTCCTCAAATTGAGTGTTTCCAAG
gcttaat putative branch site (score: 4)
ttaattttgttgtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaataaaataagctttaaactaactatcttaaacaaaacgcttcttgattctcaatattctgttttcttgatttcttggatctttggttcttgattcttgaaacctgaatcttttatttttggcttaattttgttgtattatacgtctatggttgttggcagGTGGATTAAGGTACCATGGGATGGCACCATTGATCTCACATGTTTATGAACAAGGATTCATGGAAGCAATTTCAATTCCTCAAATTGAGTGTTTCCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA