Sequence
atgc intronic sequence ATGC exonic sequencegtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G26510.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 11
gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaac-ttgatggtgttttgaaataa--tgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
| | || |||| || |||| | | | | | | | | || | | || | | || ||| | | ||||||||||| ||||||||||| || || ||||| || |||||||| || || |||||||| || |||||||||||||| |||||||| |||||
-----attcaatttcttgttaaagattctgttaataaagctcttcatacatccttgagtataaatacataactattgtcaattatttcttacaattgctttccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGTAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGAGAAGGAGACAATGGCAAACAG
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os02g17320.2 (Oryza sativa), 3'ss of exon 11
--gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaa--taatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
| | ||||| | || | | ||| || | | || || | ||| | || | | || | || || | || || || | | ||||||||||| ||||||||||| || || ||||| ||||||||||| || || |||||||| || |||||||| ||||| |||||||| |||||
ggattcattcct-tgtcaagtatcttgttagta----aagcacatcataaatttttga-atagaaaggcataactatgttaattattttctgcaacttctctccagTGGTGAGAGTATGGAGAATGCATTGCGGGCATGCTGCAAAGGTATAAAAATTGGGAAGATTCTTATTCACAGGGAAGGAGACAATGGCAAACAG
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G034143_T03 (Zea mays), 3'ss of exon 12
gtactttcctatatcttagctt-tagtttataca-ataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
| | ||| | | | | | ||| || || | ||| |||||| ||| |||| | || |||| || | | | | ||||| || |||||||||||||||||||||||||| || |||||||| ||||| |||||||| || ||||| | ||||| |||||||| ||||||
ttcatgcactagaattcaattcatcacaagaacatgtatgatcccccctatccttgaataaagtgtactct-gcaaa--tgatt-tgctacaactgctttccagTGGCGAAAGCATGGAGAATGCGTTACGAGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGAGACAATGGACAACAG
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 10
gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataa-----tgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
|| | | || || ||| | |||| | | | ||| | | || |||| | || | | ||||| || || ||||||||||| |||| ||||| || |||||||| ||||| |||||||| || ||||| | |||||||||||||| ||||||
-------aacatgcacaattgacccctcatgcactagaattcaattcatcagtcatcacaagaacatctatgtactctacaaatgatttgctacaactggtttccagTGGCGAAAGTATGGAGAATGCACTACGTGCATGCTGTAAAGGTATAAAGATTGGGAAGATTCTTATTCATCGGGAAGGTGACAATGGACAACAG
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 11
--gtactttcctatatcttagctttagtttatacaataggaacttccccatcct-ttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
| |||||||| | | | |||| | | || || || | | || | | | || | | | || ||||| | | |||| ||||| ||||| ||||| ||||| |||||||||| ||||||||||||||||| ||||| || || ||||| ||||||||||||||||||||||||
ttcttctttcctaattactcggtttaatgtggacc-tatgatcactgcaattttatataaatagaatttgtccttaaatttgata----tgcaatctaatttcagTGGGGAGAGTATGGAAAATGCTCTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCTTATTCATAGAGAAGGTGACAATGGTCAACAG
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 11
gtactttcctatatcttagctttagtttatacaataggaacttccccatcct----ttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG-
| || | | ||| | || || | || | | || | ||||| | | | | || | | || | | | |||| ||||| ||||| ||||||||||| || ||||||| || |||||||||||||| ||||| || |||||||||||||||||||||||||||| |||
---ccttaagaaaccttgtgtgtatctt-tgcagtctataatttattgtttagaaattcatttactattatcataattaaaaaat--taatatatgctaatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATCAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAGG
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA08G45270.1 (Glycine max), 3'ss of exon 11
------gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
| | | | | ||| || |||||||| || || | ||||| | | | || | | | | | | | | || ||||| ||||| ||||||||||| || ||||||| || |||||||| ||||| ||||| || |||||||||||||||||||||||||||| |||
ccctaagaaaccttgtgtgtctct-ctgcagtttataattta-----ttgttaagaaattcattttctgttatcataattaataatt--taatatatgctcatttcagTGGGGAGAGTATGGAGAATGCTTTGAGAGCATGCTGTAAAGGTATAAAGATTGGGAAAATTTTAATTCACAGAGAAGGTGACAATGGTCAGCAG
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA14G01480.1 (Glycine max), 3'ss of exon 8
---------------------------------------gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
| |||||||| | | ||| | | || || || | | || ||| | | | | | || || || || | | | |||| ||||| ||||| ||||| ||||| ||||||||||| ||||||||||||||||| ||||| || ||
ttgaaaatattatccaacctatattctaagaaactagttcttctttcctaattactcagtttgatgtgaacc-tatgatcactgcaattttttataaacagAATTTGTCCTTAAATT--TGATATGC-AATCTAATTTCAGTGGGGAGAGTATGGAAAATGCTTTACGAGCATGCTGCAAAGGTATCAAGATTGGGAAAATTCT-------------------------------
upper sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 11
---gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
| | | | || | || ||| | || || | | || | | ||| || | | || | | |||| ||||||||||| ||||||||||| || ||||||||||||||||||||||| || |||||||| || || || || ||||| || || ||||| |||
aaaggaaaaagaagtgcaaaaagcatattcctggttat-ggacccattttctctttgtcttttgcattttggtttgaacc--atcttctctt--actgatgccagTGGTGAGAGTATGGAGAATGCTTTGCGAGCATGTTGCAAAGGTATCAAAATTGGGAAGATTCTTATCCATAGGGAAGGGGATAACGGTCAGCAGMapped 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|125244484|gb|EL258569.1|EL258569EST: TCTGGTGTGGATTTCTGTAAACGGTTATGTGGTGTCTCGGTGATTAGGAG TGGTGAGAGCATGGAGAATGCGTTACGAGCA
genomic: TCTGGTGTGGATTTCTGTAAACGGTTATGTGGTGTCTCGGTGATTAGGAGgtactttcct ... ataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
tgttttgaaataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactttcctatatcttagctttagtttatacaataggaacttccccatcctttcatatcccactctctcaccaacttgatggtgttttgaaataatgctagTGGTGAGAGCATGGAGAATGCGTTACGAGCATGTTGCAAAGGTATCAAGATCGGGAAGATCCTAATTCACAGAGAAGGTGACAATGGTCAACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA