Sequence
atgc intronic sequence ATGC exonic sequence...ttaatgcataaatgttatatacttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G21050.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------ttaatgcataaatgttatatacttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaat-agGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
|||| | || | | ||| | | || |||| || ||| | | || || |||| || || || |||| || ||||||||||| || || || | ||| |||| | |||||||| ||||||||||||||||| ||||| |||||||| || |||||||||||
gtagtacaacacaaaagcaccatctgttagcatgcagcatgcttgcatttctcgtctgaatagcgaggcgcatgcctgaacattattacattgcgttgtgctgaaaaaacacttgtgttttttgtatgaatatcagGTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGT
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G149481_T03 (Zea mays), 3'ss of exon 5
----------ttaatgcataaatgttatatac---ttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT--
|| | || | |||| | ||| | ||| | | | | | | | |||| ||| | || || || | |||| || || |||||||| || || || | |||| |||| | |||||||| ||||||||||||||||| ||||| ||||| || || |||||||| ||
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTGT
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G149481_T02 (Zea mays), 3'ss of exon 4
----------ttaatgcataaatgttatatac---ttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
|| | || | |||| | ||| | ||| | | | | | | | |||| ||| | || || || | |||| || || |||||||| || || || | |||| |||| | |||||||| ||||||||||||||||| ||||| ||||| || || |||||||| ||
gtacgcaagcgtagcgttgaagcataatatgcattctgtgggcctgtggcctgtggcctgtgggtgaccggccgagacgatgtg-tgtgcttctgctgctctacttgttgcagGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGT
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 4
-------------------------------ttaatgcataaatgttatatacttgta----gagttgtagataat-tgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
|||| || | | |||| | || | || | || || |||| | || | | ||||| |||| | | || || ||| | |||||||| |||||||| || || | ||| ||||| |||| || || ||||||||||||||||| ||||||||||| |||||||||||||||||
gtgacaacaatattcataaattaagttacaaataatttattattattattatttcatacattaaattattaatgatatgaaactgtcattaatatagtagtaatgctatgtttttccaattgt-tattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 4
--------------------------------ttaatgcataaatgttat--atacttgta--gagttgtagataat-tgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
|| | ||| | | |||| |||| || | || | || || || | || || | ||||| ||| | | | || || ||| | |||||||| |||||||| || || | ||| ||||| |||| || || ||||||||||||||||| ||||||||||| |||||||||||||||||
gtaacaataataaatttacaaacagatacgtactactacattattattattattactgatattcaattattaattatatgcaattgtaattaatttagtagtaatgctatgcttttccgattgt-tattatgcttagATGGAAGGAGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTCGGGGGACATGCTGTTACTGT
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 4
------------------------ttaatg--cataaatgttatatacttgtagagttgtagataattgaattttcttataga-aggagaataatgtaatgtaccaatgttggaata-ataa--aaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
| ||| |||| || |||| || | | || ||| ||| | | | | | |||||| | | ||||| ||| || | ||||| |||||||| |||||||| || || | ||| ||||| |||| || || ||||||||||||||||| |||||||| || |||||||| ||||||||
gtaataataatttagatttgcaaataaataatcatatatattattcctactgtgatctatgaatcattatgtttcttagtggctactataataatatgcgatcttgatgttactatatatgattgtgtagGTGGAAGGAGTTAAGCATTCGGGCCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTTGGGGGACATGCCGTTACTGT
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 4
----------------------------ttaatgcataaatgt-----tatatacttgtagagttgtagataattgaattttcttataga-aggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
| |||||||| || | |||||| | || | | | || ||| |||| | | | | | |||||| | | ||||| || || ||||| || || || |||||||| || || | ||| ||||| |||| || || ||||||||||||||||| |||||||| || |||||||| ||||||||
gtaataacaatttagatttgcaaataaataaatgcatatatatacatatatatatatatatatatatgaattattatatttattagtggctactataataatatgcgatcttgatgttactatgattgtg-tagGTGGAGGGGGTTAAGCATTCGGGTCCGACCAAATTGGTTCTATATTTTACGGGGGCCACAAACATTCTCTACACATTTGGGGGACATGCCGTTACTGT
upper sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 4
ttaatgcataaatgttatatacttgtagagttgtagataattgaattttcttatagaaggagaataatgta-atgtaccaat--gttggaataataa-aaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
|| | | | || | || | | | | | | || || || || | || | | || || || || | ||| || | ||||||||||| || ||||| ||| ||||||||| |||||||||||||||| ||||||||||| ||||||||||| ||||||||||| |||||
gtactatacatatatctcattcaaccaaatatccaaaacatatgatattaaaattagtaaatgattttatttatttatttatttatttatttgttaatgggcagATGGAAGGAGTGAAACACTCAGGTCCATCCAAGCTGGTGCTATACTTCACAGGGGCTACAAACATTCTCTACACATTCGGGGGACATGCTGTGACTGTMapped 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|125037067|gb|EL109336.1|EL109336EST: CCACTTACACTGCTTGGTACCTCACCATTGCCTCTATCCTCCATGGACAG GTAGAAGGAGTGAAGCATTCAGGACCAAGCAAG
genomic: CCACTTACACTGCTTGGTACCTCACCATTGCCTCTATCCTCCATGGACAGgtaactagtt ... ataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
aatgttggaataataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaatgcataaatgttatatacttgtagagttgtagataattgaattttcttatagaaggagaataatgtaatgtaccaatgttggaataataaaaatagGTAGAAGGAGTGAAGCATTCAGGACCAAGCAAGCTGGTTTTATACTTCACAGGGGCCACAAACATTCTTTACACATTCGGTGGACATGCTGTTACTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - -gcataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaggaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaccaa