Sequence
atgc intronic sequence ATGC exonic sequence...ctaacttaaatgttctctttggaacatgaattatcacatatcgtttgttttgtactggtttctgtaatcatcataacatatttttcccttttaattgcagCTCCACCACTGAAATTGATTGATTTGCCTGGACTGGACCAGCGAATTGTGGACGATTCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G59610.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 4
ctaacttaaatgttctctttggaacatgaattatcacatatcgt-ttgttt--tgtactggtttctgtaatc--atcataacatatttttcccttttaattgcagCTCCACCACTGAAATTGATTGATTTGCCTGGACTGGACCAGCGAATTGTGGACGATTCTATG--------------------------------------
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---------------------gtaagcccattatcatattctatgttgctccatgcattggatcatgaaacttaatcattttgtcctgttctaaattt-ctacagCACCTCCATTGAAATTGATTGACTTGCCTGGATTGGACCAGCGGATAGTGGATGACAAAATGGTGAGTAGGTATATGTTATCTTGTCCTAAGTTTAAATT
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G40300.2 (Glycine max), 3'ss of exon 4
ctaacttaaatgttctctttggaacatgaattatcacatatcgt-ttgttt--tgtactggtttctgtaatc--atcataacatatttttcccttttaattgcagCTCCACCACTGAAATTGATTGATTTGCCTGGACTGGACCAGCGAATTGTGGACGATTCTATG
| | ||||||| || | ||| | || | ||| | || || ||||| | | ||| || | |||| || ||| ||||||||||||| ||||||||| |||||||||| || ||||| || |||
---------------------gtaagcccattatcatattctatgttgctccatgcattggatcatgaaacttaatcattttgtcctgttctaaattt-ctacagCACCTCCATTGAAATTGATTGACTTGCCTGGATTGGACCAGCGGATAGTGGATGACAAAATG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 4
-----ctaacttaaatgttctctttggaacatgaattatcacatatcgtttgttttgtactggtttctgtaatcatcataacatatttttcccttttaatt--gcagCTCCACCACTGAAATTGATTGATTTGCCTGGACTGGACCAGCGAATTGTGGACGATTCTATG
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gtaagcccattataatattctatgttgctcccttcct-ttatgcttacattacat-gtattggcatcatgaaacttaatctctttgttctgttctaaaattctacagCGCCTCCATTGAAATTGATTGACTTGCCTGGATTGGACCAGCGGATAGTGGATGACAAAATG
upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 4
--ctaacttaaatgttctctttggaacatgaattatcacatatcgtttgttttgtactggtttctgtaatcatcataacatatttttcccttttaattgcagCTCCACCACTGAAATTGATTGATTTGCCTGGACTGGACCAGCGAATTGTGGACGATTCTATG
|| || ||| | ||| || | || || | | || | | | || ||| | | | |||| ||| | | ||||||||||| ||||||| || ||||| |||||| |||| || || |||||||| ||||| |||
tgctgttctatgtgtgcatattgtttgttgtttcattttttacactccttgttttcactgatgatggaat--ttcttttctggttttttcttcatactccagCTCCACCATTGAAATTAATCGATTTACCTGGATTGGATCAACGCATTGTGGATGATTCAATGMapped 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|86063710|gb|DR359467.1|DR359467EST: TTCGTACCAGCACAG CTCCACCACTGAAATTGATTGATTTGCCTGGAACTGGACCAGCGAATTGTG
genomic: TTCGTACCAGCACAGgtaattcctt ... ttaattgcagCTCCACCACTGAAATTGATTGATTTGCCTGG-ACTGGACCAGCGAATTGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttgtactggtttctgtaatcatcataacatatttttcccttttaattgcagCTCCACCACTGAAATTGATTGATTTGCCTGGACTGGACCAGCGAATTGTGGACGATTCTATG
catatttttccctttt CT-rich tract
taatcatcataacata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctaacttaaatgttctctttggaacatgaattatcacatatcgtttgttttgtactggtttctgtaatcatcataacatatttttcccttttaattgcagCTCCACCACTGAAATTGATTGATTTGCCTGGACTGGACCAGCGAATTGTGGACGATTCTATG
- -acttaaa
- - - - - - - ctctttg
- - - - - - - - - - - aacatga
- - - - - - - - - - - - - - - - - cacatat
- - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcataa