Sequence
atgc intronic sequence ATGC exonic sequencegttagttgaattgccctcttcgcttaggtgttttgttatgtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13520.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os03g60460.1 (Oryza sativa), 3'ss of exon 2
-----------------gttagttgaattgccctcttcgcttaggtgttttgttatg--taatg---tttacaataatggtcat-----ctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
|| ||| | | || || | | ||| | | |||| ||| || | | ||| | | || | || | ||||||| || |||| ||||| |||||||| ||||| ||||| | || || ||||||||||| || || ||| | ||||| ||||||||||||||| | |
gtgagtgcaaaattgcgactatttgtttcaactgttttgcaacgttctttaatcaaaatcaatgagtttttcatgacttgtcgtgatgtttcattctttttcccctgttagATTGGTCGACCTGCATTTGATGAATTCCTGAAGAATTACATATCCACATTTAAGTTCAAGTCGATAGACACAGAGACATTCCTTGAATTCCTGAAAACCA
upper sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G139662_T01 (Zea mays), 3'ss of exon 1
------------------------------------gttagttgaattgccctcttcgcttaggtgttttgttat-gtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
|| ||| | || | | | | || ||| | | | || | | || | ||| | | ||||||||| ||| ||||||| ||||| || | ||||| |||||||| || ||||||||| | ||||| |||||| | ||||||||||||||||| ||| | |
gtgggtggaagtatggaacatggcaactcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgcttgtatcagATTGGCAGACCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA
upper sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G035346_T01 (Zea mays), 3'ss of exon 1
------------------------------------gttagttgaattgccctcttcgcttaggtgttttgttat-gtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
|| ||| | || | | | | || ||| | | | || | | || | ||| | | ||||||||| || ||||||| ||||| || | ||||| |||||||| || ||||||||| | ||||| |||||| | ||||||||||||||||| ||| | |
gtgggtggaagtatggaacatggcaactcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgcttgtatcagATTGGCAGGCCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCAATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA
upper sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G155580_T01 (Zea mays), 3'ss of exon 2
------------------------------------gttagttgaattgccctcttcgcttaggtgttttgttat-gtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
|| ||| | || | | | | || ||| | | | || | | || | ||| | | ||||||||| || ||||||| ||||| || | ||||| |||||||| || ||||||||| | || || |||||| | ||||||||||||||||| ||| | |
gtgggtggaagtatggaacatggcaactcttctactcttccttgcaacattctttcagtaaaattacttcagtattggactaatttctaacgtgatgtcttatgcatgttgcttgtatcagATTGGCAGGCCTGCTTTCGACGAGTTTTTAAAGAAGTACATTGCAACCTTCAAGTTCCAATCGATAGATACAGAGACATTTCTTGAATTCCTCAAAACCA
upper sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G38780.1 (Glycine max), 3'ss of exon 2
-------------gttagtt--gaattgccctcttcgcttaggtgttttgttatgtaatgtttacaataatggtcatctatttactggaaaacttt-cagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
|| | | || || || || | | || | | || ||| | | | |||| || | ||| |||| ||| |||| ||||| || || || |||||||| |||||||| ||||||||||| || || ||||| | ||||| ||||| ||||| ||||| |
gcatgctttgtttgtcattcaggagttaaacttgaacctaatttattggaattaggtatttttttttctttatttgttaattttcttatggatgggacagGTTGGGAGACCTGCATTTGATGAGTTTCTGAAGAAATATATTGCTACCTTCAAGTTCAAATCCATTGATACCGAAACATTCCTTGACTTCCTTAAAGCCA
upper sequence: AT5G13520.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv13s0067g03300.t01 (Vitis vinifera), 3'ss of exon 2
gttagttgaattgccctcttc--gcttaggtgttttgttatgtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
|| |||| ||| | | | || | ||| | ||| || | | | | |||| | | || | || ||||||||||||| |||| ||||| |||||||| |||||||| |||| || ||||||||| | ||||| || ||| | | ||||| ||||||||| | |
gtatgttggtttgacagttagaggttttgaggttgttcaatgaaaaaat-atgagattggttgtgttttgtttcttgaatgttcagATTGGAAGGCCTGCATTTGATGAATTCCTAAAGAAATATATTGGCACCTTCAAGTTCCAATCAATTGACACAGATATGTTTCTAATTTTCCTGAAAACGAMapped 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|164085210|gb|ES104158.1|ES104158EST: GTCCCATATGAAAAAGGATTCCAATTTGTGTTGCGAATTGAAACGACCAG ATTGGAAGAACTGCTTTTGACGAATTCC
genomic: GTCCCATATGAAAAAGGATTCCAATTTGTGTTGCGAATTGAA-CG-CCAGgttagttgaa ... aaactttcagATTGGAAGAACTGCTTTTGACGAATTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttttgttatgtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
ctttc CT-rich tract
ttatgtaatgtttaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagttgaattgccctcttcgcttaggtgttttgttatgtaatgtttacaataatggtcatctatttactggaaaactttcagATTGGAAGAACTGCTTTTGACGAATTCCTCAAGAAATACATTGCTACTTTCAAGTTCAAGTCAATCGATACAAACACATTTCTTGAATTCCTGAAAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA