Sequence
atgc intronic sequence ATGC exonic sequencegtatgttttccttaacaagtatccatgttataatatcagattacataaactgcttgatttcatatcctgttccttgtttttttccagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTTGAGAAAATACTTGCTTTACTGTTCAACCACTGTGAAAGCGAGGAAGAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G02560.2 |
intron # | 22 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 23
------------------------------------gtatgttttccttaacaagtatccatgttataatatcagattacataaactgcttgattt----catatcctgttc-cttgtttttttc---cagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTTGAGAAAATACTTGCTTTACTGTTCAACCACTGTGAAAGCGAGGAAGAAG
| | ||| || | ||| || | | || | | | || | || |||| |||| | ||| |||| | | ||||| ||||||||||| ||||| |||||||| || || || | ||||| || |||||||||||| |||||| ||||||||||||||||| |||||||| |
gtgtgttgccttaacaaaatctatctggttaatttgatttctttctaatatttaatatatatatgcaatcatgaaaacttgtgaa-tatttaatttaatatatatacaattctcttgcccctacctggcagGTAATTGTGAGACAATCTGTAGATAAAGCAGAGTTTCAAGAGTCCAGTGTGGAGAAAATACTTAATTTACTCTTCAACCACTGTGAAAGTGAGGAAGAGG
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 22
---------------------gtatgttttccttaacaagtatccatgttataatat-caga---ttacataaactgcttgatttcatatcctgttc-cttgtttttttc---cagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTTGAGAAAATACTTGCTTTACTGTTCAACCACTGTGAAAGCGAGGAAGAAG
| || || || | | || | | | |||||| ||| | | ||||| || | | |||| | ||| |||| || | ||||| ||||| ||||| ||||| |||||||| || || || | ||||| || |||||||||||| |||||| ||||||||||||||||| |||||||| |
gtgtgttgccttaacaaaatcatctggttggttttatttctttctaagatttaatatatagacaatcatgaaaactcatttaatatatatgcaattctcttgcccttacctggcagGTAATTGTCAGACAATCTGTGGATAAAGCAGAGTTTCAAGAGTCCAGTGTGGAGAAAATACTTAATTTACTCTTCAACCACTGTGAAAGTGAGGAAGAGG
upper sequence: AT2G02560.2 (Arabidopsis thaliana), 3'ss of exon 22
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 23
gtatgttttccttaacaagtatccatgttataatatcagattaca-taaactgcttgatttcatatcctgttcc--ttgtttttttccagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTTGAGAAAATACTTGCTTTACTGTTCAACCACTGTGAAAGCGAGGAAGAAG
|||| || | | ||| | || || |||| ||||| || | | | ||| || || ||| || || | || || |||||||| ||||| || || || || ||||| || || ||| |||| || |||||||| |||||| ||||| || |||||||||||||| |||||||| |
gtatattgttttgaactacaattgat-ttatgttatcaaatggtacttacctggttttttatttattaatttatggttttcttcttgcagGTTATAGTGAGGCAATCGGTAGACAAAGCAGAGTTTCAGGATTCTAGTGTTGAGAAGATACTTAAATTACTTTTTAACCACTGTGAAAGTGAGGAAGAGGMapped 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|86061724|gb|DR357481.1|DR357481EST: TCGATAATCAACAGAAAAAACAATATATTCTCCTTCATTCACTCAAGGAG GTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTT
genomic: TCGATAATCAACAGAAAAAACAATATATTCTCCTTCATTCACTCAAGGAGgtatgttttc ... ttttttccagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTT
EST:
gi|164086131|gb|ES105646.1|ES105646EST: ATTCACTCAAGGAG GTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGTGTT
genomic: ATTCACTCAAGGAGgtatgttttc ... ttttttccagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atatcagattacataaactgcttgatttcatatcctgttccttgtttttttccagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTTGAGAAAATACTTGCTTTACTGTTCAACCACTGTGAAAGCGAGGAAGAAG
gcttgat putative branch site (score: 5)
tttcatatcctgttcc CT-rich tract
attacataaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgttttccttaacaagtatccatgttataatatcagattacataaactgcttgatttcatatcctgttccttgtttttttccagGTTATTGTGAGACAGTCTGTTGATAAAGCGGATTTCCAGAATTCCAGCGTTGAGAAAATACTTGCTTTACTGTTCAACCACTGTGAAAGCGAGGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG