Sequence
atgc intronic sequence ATGC exonic sequencegtaagtctcttgatcgattttcaaaggttataatttatttatcgttagtgaggctagcaggtttgtttacttattgctcatattactttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G05090.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G05090.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA10G30050.1 (Glycine max), 3'ss of exon 12
-----------------------------gtaagtctcttgatcgattttcaaaggttataatt-tat------ttatcgttagtgaggctagcaggtttgtttacttattgctcatattactttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG
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gtatgattactgatattaatcatcaccaactaattctacttacacagttacacttgtttcggttatataagattttagccctacctagttttttttttatgtttattttctacccatactgcttcagGTTAGCAATATTCCAGCATGGTTCACAGTGGATACTAGACTTGGATGTTTGTCTGTACATTTGGACACTCCTCAATGTTTTTCTGGTGAGATGTATTCTG---
upper sequence: AT3G05090.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA19G42990.1 (Glycine max), 3'ss of exon 13
--------------------------------------gtaagtctcttgatcgattttcaaaggttataattt---atttatcgttagtg-aggctagcaggtttgtttactt-attgctcatattactttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG
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gtatgattactgatttacctcattgatttcattttaaaatatatttttttcttggctagaaaacatgacgatttccaatagtttatttgttcaagttggcttttaattttcctccaatgct-gcattgctgctttagGTTAGTATTCCTGCATGGTTCACAGTGGATACCAGGCTTGGAAGCTTGTCAGTCCATTTGGACACTCCTCAATGTTTCTCTGCAGAGATGTATTCAGCAG
upper sequence: AT3G05090.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 13
gta-agtctcttgatcgattttcaaaggttataatttatttatcgttagtgaggctagcaggtttgtttacttattgctcatattactttctt-agGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG
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gtatggattcctaatttatattaaa------tatttgttgtaatttgagtgaaacattttggtggatctttcttttgattgcattatcttgtccagGTGAGCATTCCTGCATGGTTTACTGTAGATACGAGGCTGGGAAGCTTGTCTGTCCATTTGGATACCCCACAATGCTTTTCTGCAGAAATGTACTCTGCTGMapped 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|124791685|gb|EH881364.1|EH881364EST: TCATTTGAAGAGAAGAAAGAAGAACTGTTTGAGATG GTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCT
genomic: TCATTTGAAGAGAAGAAAGAAGAACTGTTTGAGATGgtaagtctct ... actttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCT
EST:
gi|164000107|gb|ES014116.1|ES014116EST: AAGAACTGTTTGAGATG GTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATC
genomic: AAGAACTGTTTGAGATGgtaagtctct ... actttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATC
EST:
gi|116484027|gb|EG526619.1|EG526619EST: ATTTCATTTGAAGAGAAGAAAGAAGAACTGTTTGAGATG GTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCT
genomic: ATTTCATTTGAAGAGAAGAAAGAAGAACTGTTTGAGATGgtaagtctct ... actttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcgttagtgaggctagcaggtttgtttacttattgctcatattactttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG
ttactttctt CT-rich tract
tttgtttacttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtctcttgatcgattttcaaaggttataatttatttatcgttagtgaggctagcaggtttgtttacttattgctcatattactttcttagGTAAGCATTCCATCGTGGTTTACTGTGGATACACGACTTGGATGCTTATCTGTACATTTGGAGACTCCACAATGCTTCTCTGCTGAAATGTATTCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA