Sequence
atgc intronic sequence ATGC exonic sequencegtgagtctttttacttctgttttttcattcttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G13920.4 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA17G06110.1 (Glycine max), 3'ss of exon 2
-----------------------------------------------------------gtgagtctttttacttctgttttttcattcttg----agtgtgttctctccgcatgctctagctgctaattgtactgtattgata---------cagACTTGAG---GGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGG--------
|| || || || || || || ||| || |||| | | || || | | |||| | | |||| | ||||||| | | | || ||||||||||||||||| || ||| |||| || ||||| || |||||| | || ||||| ||||||||||
gtaagattttttatttttattattcggagcaatctggttttattattactgaaattgctgttcgtgttcttgttttgtgttggatatgattgcaacaggatgttattgctatctgttcaattttttaatggccttatatttttttttccctttcagACTTTCATCTGATGGACAGGACTTCTTCACATCCTATGACGAGGTTTATGATAGTTTTGACGCTATGGGTTTGCAGGAGAATCTTCTCAGGGGAATTTAC
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv11s0016g01920.t01 (Vitis vinifera), 3'ss of exon 1
----------------------------------gtgagtctttttact--tctgttttttcattcttgagtgtgt---tctctccgcatgctctagc-tgctaattgtactgtattg-----------------atacagACTT--GAGGGACAAG-ATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGG--------
| | ||| || | |||||||| | | | | | | ||| | || ||| |||||||| | | | ||| |||||| ||| | || | || ||||||||||| |||||||| ||| |||| || |||||| | |||||| | |||||||| |||||||| |
gtaaggaatacactcctcttttttctttccctccctttttttttataatactctgttttgaaaatttcaaatttaaaagtctacctatgtgtaataggatgctaattttcttttcttggttttatgaatcgatgcatacagGCTTTCAACTGATGGACAGGATTTCTTCACATCTTATGATGAGGTTTATGATAGTTTTGATTCTATGGGTTTGCAAGAGAATCTTCTCAGAGGCATTTAT
upper sequence: AT3G13920.4 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S383_1V6.3 (Physcomitrella patens), 3'ss of exon 2
------------------gtgagtctttttacttctgttttttcattct-tgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGG--------
| | | ||| | |||| ||| |||| ||||| | || || | | | || | || | | | | |||||| ||| | | | | || || || || |||| ||||| | |||||||||||| ||||||||||||||||
ccccaaaagcattggatcttaaatttttcgggggcgaattttctatttcatgagagtgtttctttcgaatcccactaacccgatttttgcttgagctcagCTTGAGCGGCGAGGGAGATGATTTCATTTCTACTTGGGAAGAGGTCCACGAGACGTTTGACGTCATGGGTCTTCACGAGAACCTTCTCAGGGGTATATACMapped 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|116436248|gb|EG478840.1|EG478840EST: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT ACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
EST:
gi|86035160|gb|DR330913.1|DR330913EST: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGT ACTTGAGGGACAAGATGAGTTCTTCACATCSTATGATGATGTTCATGAGAG
genomic: GAAGGCACACAGTTTGATGCACGTCAGTTTGACCAGAAACTCAATGAAGTgtgagtcttt ... attgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGG
taattgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtctttttacttctgttttttcattcttgagtgtgttctctccgcatgctctagctgctaattgtactgtattgatacagACTTGAGGGACAAGATGAGTTCTTCACATCCTATGATGATGTTCATGAGAGCTTTGATGCCATGGGTCTTCAAGAGAACCTTCTCAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA