Sequence
atgc intronic sequence ATGC exonic sequencegtgagtgctttatgtaagcgatacgttttcaacaagttgtgtactgtgtttgttacttggatttatttgttgaattgagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
Basic information
species | Arabidopsis thaliana |
transcript | AT1G63610.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G63610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g58650.1 (Oryza sativa), 3'ss of exon 3
-------------------------------gtgagtgctttatgta-agcgatacgtttt-----caacaagttgtgtactgtgtttgt-tacttgg---atttatttgttgaat-----tgagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
| || || |||| || || || | || | | | | | ||||| ||||| || | |||| || | | || | || | |||||||||| || || || ||||| ||| || || ||||||| ||||| ||||| || || || || |||||||| ||||||||||| ||||||||||
gtaatgggatatcatatgttcaggtcttgacgccggtttttcttgtatggcattatgtcatactactaattattagcacaattcatttgtacacttgagccatgaaattgtgacatgtttatttacctttttcatcgacacagGTTGCTGAAAATCTAGCTCAGCTTATGTACAGTGTTCTGATGACCGGATACATGTTCAGGAATGCGCAGTATCGTCTGGAATTGCAACAGAGTTTGGAGC
upper sequence: AT1G63610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G140809_T01 (Zea mays), 3'ss of exon 3
---gtgagtgctttatgta---agcgatacgttttcaac--aagttgtgtactgtgtttgttacttgga---tttatttgttgaatt-----gagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
||||| | | | | | | | || ||| || | | | | || || | ||| ||| |||||| || || || | ||| |||| ||||| || || || ||||| ||| || || | ||||||||||| |||||||| || || || || ||||| ||| ||||||| ||||||||||
gtattgagtacctcctattcctatggctgttttcccaatggaaaatttacattttgcatgacatttgtgtcttttgattgttgctttgttacgattatcttttatcaaaacagGTCGCTGAAAATCTGGCTCAGCTTATGTACAGTGTCCTAATGACTGGATACATGTTTAGGAATGCACAGTACCGTCTGGAACTGCAACAGAGTTTGGAGC
upper sequence: AT1G63610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA06G02100.1 (Glycine max), 3'ss of exon 3
gtgagtgctttatgtaagcga-tacgttttcaacaagt--tgtgtactgtgtttgttacttggattt---atttgttgaattgagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
|| | | | | || || | | | | || | |||| | | || || | || | | | |||| || |||||| ||||| |||||||||||||| ||| ||| | ||||||||||||| ||||| | || || ||||| ||| | ||||||||| |||||||||| |
---gttgagccacgcggttgggttgaattgcagttattcctttttatttattttgctccatgcatcttacatatctcaggggaatcatttggctttttattagGTAGCTGAAAACCTTGCACAGCTCATGTACAGCATCATGATGACTGGATACATGTTCAAGAATGCGCAATACCGTTTGGAATTGCAAGAAAGTTTGGAAC
upper sequence: AT1G63610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv18s0001g00090.t01 (Vitis vinifera), 3'ss of exon 3
---------------------------------------------------------gtgagtgctttatgtaagcgatacgttttcaacaagttg-tgtactgtgtttgttacttggatttatttgttgaattgag--cattatatattgcttt-agGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
| | ||| ||| | ||| | || || |||| || |||| || | || ||| | | | || || | | || |||| |||||||||| || ||||| ||||| ||| || || ||||||||||||||||||||| || ||||||||| | | ||| ||||||||||||||||||
gtaagtttgttactatctcatgaacatggatttcagaggagttataagtgattaatgccggtttgtttttgtgttcatattttttgtattaatctgatgtaatgggtttccaacctccatgtatgttataatctggaatcacttggttttcctttcagGTTGCTGAAAATCTTGCCCAGCTCATGTACAGTGTTATGATGACTGGATATATGTTTAAGAATGCTCAATATAGGTTGGAACTGCAACAAAGTTTGGAGC
upper sequence: AT1G63610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S207_10V6.1 (Physcomitrella patens), 3'ss of exon 4
gtgagtgctttatgtaagcgatacgttttcaacaagttgtgtactgtgtttgtt--acttggatttatttgttgaattgagcattatatattgcttt--agGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
|| || | | | | ||| | || | ||||| | | | ||| || | | | | ||| | | | | || | ||||||||||| || ||||| ||| |||||| ||||||||||||| ||||| || |||||||| ||||| || ||||||||||| || ||| |
-tgtatggtaagcctgaagagcagttttatacgccgtcacatggagtgttagcttaatctggtactaacaggagtttactgtattttgaaacattgtgcagATAGCTGAGAACCTAGCGCAGCTCATGTACAGCGTGATGATGACTGGATACATGTTCAGGAACGCTCAGTATCGACTAGAATTGCAACAGAGCTTGAGCC
upper sequence: AT1G63610.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: EFJ23149 (Selaginella moellendorffii), 3'ss of exon 3
gtgagtgctttatgtaagcgatacgttttcaacaagttgtgtactgtgttt-gttacttggatttatttgttgaattgagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
||| || ||| ||| |||| | || || | | || | | | | | ||||| |||||||| ||||| ||||| ||| ||||| | ||||| ||||||||||||||||| || ||||| ||||| || |||||||||||| | || |
----------------------------------------gtaatggttttagtttgttggtccttcttcgtggttaaaacact-tgtgcttttctagGTGGCTGAGAATCTTGCTCAGCTCATGTATAGCGTCCTAATGACAGGATATATGTTTAGAAATGCGCAATACCGTCTCGAGTTGCAACAAAGTCTAGAACMapped 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|124915167|gb|EH989041.1|EH989041EST: ATATGATTGGAACGCTGCCACCGCAGTTTTTCGCCGTTACTGTCACCTCT GTTGCTGAGAACCTTGCACAG
genomic: ATATGATTGGAACGCTGCCACCGCAGTTTTTCGCCGTTACTGTCACCTCTgtgagtgctt ... attgctttagGTTGCTGAGAACCTTGCACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgtgtttgttacttggatttatttgttgaattgagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
ttgcttt CT-rich tract
atttatttgttgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtgctttatgtaagcgatacgttttcaacaagttgtgtactgtgtttgttacttggatttatttgttgaattgagcattatatattgctttagGTTGCTGAGAACCTTGCACAGCTGATGATGAGCGTGTTGATGACTGGATATATGTTTAGAAACGCTCAATATCGTCTTGAATTGCAACAAAGTTTGGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG