Sequence
atgc intronic sequence ATGC exonic sequenceTTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttctttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT3G44850.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g53720.1 (Oryza sativa), 5'ss of exon 2
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttctttgccagtttgg---tatg-aagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag-
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ATCTGCTGACTTGTGGTCCTTTGCATGCATATGCTTTGAGCTTGCCACAGGAGATGTGCTATTTGATCCGCACAGTGGTGACAGTTATGACAGGGATGAGgtatgtctatttattt---ctttccaagacatttcatatctatacaaaacttaactcaaactatcacctgtcaacactttagcttaaaaaaataggagtctat
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G171987_T01 (Zea mays), 5'ss of exon 2
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttctttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag---
||||| || |||||||||||||| || ||||| || ||||| ||||| || ||||| | |||||||| || ||||| || |||| |||| | |||||||||| | || | | || | ||| || ||| | | | ||| | || | | || | | ||| | |
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTGCCACTGGGGATGTGCTATTCGATCCACATAGTGGCGATAATTTTGACAGAGATGAGgtatatctattttt-tttgcattccctgtttttttttctcggacatctattgtacttctcatggaactgtatccaagaaagaaagagaatcacccgaatac
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G009843_T02 (Zea mays), 5'ss of exon 3
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatat---tcactttctttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag
||||| || |||||||||||||| || ||||| || ||||| |||| || ||||| | || ||||| |||||||| || |||| |||| | |||||||||||| || | | || | | ||| | | | ||| | ||| || | | || | | | |
ATCTGCTGACATGTGGTCCTTTGCATGCATTTGCTTTGAGCTTACCACTGGGGATGTGCTATTTGATCCACACAGTGGCGATAATTTTGACAGAGATGAGgtatgtctattttttcacatcgccctgttttcatctattgtactgttgatggaaccttat-acaagaaaaaaagaaagaaaatcattcgaatacaagtgta
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G08900.1 (Glycine max), 5'ss of exon 2
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttct-ttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag------
|||||||| | |||||||||||||| ||||| |||||||| ||||| || ||||| | || ||||||||||||||||| || ||||| | ||||||||| | | | ||| | | | | ||| | || |||| |||||| || | | || || | | ||
CCCTGCAGATTTATGGTCCTTTGCTTGCATTTGCTTCGAGCTTGCCACTGGTGATGTTCTTTTTGATCCTCACAGTGGTGACAACTATGATAGAGATGAGgtaaccataactgcacctgttttgtactaaaaagaagctatttggctttattttgtg---ctattaagtatcaccacca--tgcttacaactattatgaacttgt
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA12G30440.1 (Glycine max), 5'ss of exon 2
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttc------tttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag
| | |||||| |||||||||||||||| ||||| || ||||| ||| | || ||||| | || |||||||| |||||||| || ||||| ||||||||||| || || | | | ||||| || | | || | | | |||| | | | | || | | || | | || |||
TCCAGCAGATCTGTGGTCCTTTGCTTGCATTTGCTTTGAGCTTGCCTCTGGCGATGTTCTTTTTGATCCTCATAGTGGTGACAACTATGATAGGGATGAGgtaagtgcacctgtttggactttgaaagaattggttggcttcatttcttgctctaatct-tctaatgtttgctgttaatattattattatcattattattt---
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA17G05480.1 (Glycine max), 5'ss of exon 2
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttc------tttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggt--tgcctttgtttcag
| | |||||| |||||||||||||||| ||||| || ||||| || | || ||||| | || |||||||| |||||||| || ||||| ||||||||||| || || | | | ||||| |||| | || | | | |||| ||| || | | ||| || | | | | | || |||
TCCAGCAGATCTGTGGTCCTTTGCTTGCATTTGCTTTGAGCTTGCATCTGGTGATGTTCTTTTTGATCCTCATAGTGGTGACAACTATGATAGGGATGAGgtaagtgcacctgtttagactttgaaagaatttgttggcttcatttattgctctaataatcatc--taatgtttgctgt-taatattaataataatattattt---
upper sequence: AT3G44850.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv06s0061g01050.t01 (Vitis vinifera), 5'ss of exon 2
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttctttgccagtttggtatgaagagctaagttgtatca-ctattatgtgcagtcttgaac---tggttgcc-tttgtttcag-
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TTCAGCTGATCTATGGTCCTTTGCTTGCATTTGTTTTGAGCTGGTAACTGGAGATGTTCTTTTTGATCCTCACAGTGGTGACAACTATGATAGGGATGAGgtatgt----agagatccttaatttttgcttgtggaccttggaatgcctatttttagtgtccatagaactgactttctaacatctttttaccacttattgctatMapped 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|124967374|gb|EL041414.1|EL041414EST: TCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAG GATCACCTGGCATTGATGATGGAGCTTCTAGGGATGATGCCACGAAAGA
genomic: TCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcat ... tttgtttcagGATCACCTGGCATTGATGATGGAGCTTCTAGGGATGATGCCACGAAAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTCTGCAGATATGTGGTCCTTTGCTTGTATTTGTTTCGAGCTGGCCACCGGAGATGTCTTGTTCGATCCTCACAGTGGTGAAAATTATGACCGGGATGAGgtatgttcatatatattcactttctttgccagtttggtatgaagagctaagttgtatcactattatgtgcagtcttgaactggttgcctttgtttcag
- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG