Sequence
atgc intronic sequence ATGC exonic sequencegtataattactcagggcttatactaatcaaagatgtaagaatgagtaattcgtggatgttataagcaaaagaaaaactcataacttgttggtgcatttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G55880.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G55880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g11660.1 (Oryza sativa), 3'ss of exon 4
gtataattactcagggcttatactaatcaaagatgtaagaatgagtaattcgtggatgttataagcaaaagaaaaactcataacttgttggtgcatttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
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-------------gtttgcatgcttcttatgttatttcttctgtatatttctt---tctcacatgtagaccttt--tttatgcctatgctataatcaaatatagGAAAAGAACACAAACATCAAATGCTTCTTAATGGACCCACCTGGATCTGGTCTGTTCAATAAGGTTACTAGAGGGGTGATGTACACAAAAGAGGAAGCTG
upper sequence: AT1G55880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G128744_T01 (Zea mays), 3'ss of exon 2
gtataattactcagggcttatactaatcaaagatgtaagaatgagtaattcgtggatgttataagcaaaagaaaaactcataacttgttggtgcat-ttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
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-------------------------gttagatgcttactatttttttgtttgtatattttatcc-tagataaacatcttttatgactatggtactccttatgtagGAAAAGAACAGGAGCATCAAATGTTTTTTAATGGACCCTCCTGGATCTGGTCTGTTCAATAAGGTTACCAGAGGGGTGATGTACACAAAAGAGGAGGCCG
upper sequence: AT1G55880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G01780.2 (Glycine max), 3'ss of exon 4
gtataattactcagggcttatactaatcaaagatgtaagaatgagtaattcgtggatgttataagcaaaagaaaaactcataacttgttggtgcatttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
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-----gtttaccacatccccccttcctccaggttgtagatgttctcattt--tgagtgtgaaagttatctgagttatttctggttc-----tatgttca-acagGAAAAGAATCCAAACATCAAGTGCTTCCTCTTAGATCCTCCTGGCTCTGGTTTGTTTAATAAGGTAACCAGGGGAGTGATGTACACCAAAGAGGAGGCGG
upper sequence: AT1G55880.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv19s0015g00380.t01 (Vitis vinifera), 3'ss of exon 5
gtataattactcagggcttatactaatcaaagatgtaagaatgagtaattcgtggatgttataagcaaaagaaaaactcataacttgttggtgcat-ttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
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------------gtcacttttcctctccatctttttatcaaaccttttttc-tgcacttcaattgtgcaaggaaagtcactg--tagtcattacatgttcaacagGAAAAAAGTCCAAATATCAAATGCTTTCTGATTGACCCTCCTGGTTCTGGCTTGTTCAATAAGATAACAAGGGGAGTAATGTACACTAGAGAGGAGGCTGMapped 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|86059873|gb|DR355630.1|DR355630EST: CTGCTGCGGGTACAGGCGGGACTTTAGCTGGTGTTTCAAGGTTTCTTCAG GATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGT
genomic: CTGCTGCGGGTACAGGCGGGACTTTAGCTGGTGTTTCAAGGTTTCTTCAGgtataattac ... atttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcgtggatgttataagcaaaagaaaaactcataacttgttggtgcatttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
tcataac putative branch site (score: 2)
aaaagaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataattactcagggcttatactaatcaaagatgtaagaatgagtaattcgtggatgttataagcaaaagaaaaactcataacttgttggtgcatttatacagGATAAGAATGAAAGAGTTAAATGTTTTCTGATTGATCCTCCTGGATCTGGTCTGTACAATAAAGTAACACGGGGAGTGATGTACACAAGAGAAGAAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG