Sequence
atgc intronic sequence ATGC exonic sequenceAACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaattgtggtttgatatattcatgcttgctatatttgtttatccgttttcgggtttattcttttgttggcgttaattaactgtcaagtttaaggt...
Basic information
species | Arabidopsis thaliana |
transcript | AT3G51870.1 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os01g16040.1 (Oryza sativa), 5'ss of exon 5
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaatt---gtggtttgatatattcatgcttg---ctatatttgtttatccgttttcgggtttattcttttgttggcgtta-at-taactgtcaagtttaaggt--
|| || ||| | || || | |||| | || | || |||||||| |||||||||||||| |||||||||||||| | |||| | ||| | | | | | ||| ||| || ||| | |||| | | || || || || || || || | | || | |
AAATTTTTCCGGAGAAAGGACGGAGAGCTTACTGTGTTTGGGAGACTTGCTGCTGGTGCTTGTGCGGGCATGACATCTACACTTgtaatttatttatttactcctgagcaattgtccttatatctagtttgatttgtttgtttgtgttctgatcattatgaaacttctatatatacttggctacttgctgatag
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G178460_T01 (Zea mays), 5'ss of exon 5
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaattgtggtttgata-tattcatgcttgctatatttgtttatccgttttcgggtttattcttttgttggcgttaattaactgtcaagtttaaggt----------------------------------------------------------------------------------
|| | ||| | || |||| |||| || ||| | || |||||||| ||||||||||| || |||||||||||||| | |||| | ||| | | || || | | || ||||| | | | ||| | | | ||| | | | || | | || || |
AAAATTTTCCGGAGAAAGGATGGAGAGCTTTCTGTATTTGGGAGACTTGCCGCTGGTGCTTGCGCGGGCATGACATCTACACTTgtaatttattttatctgcttactagcaaatgtccctgtatttatgtttttgtt---agatatggaatttgaatatagctggtttcttctttggtctattttttcatgatacataatttttttcgaaatccacagaacaccatttttagcacattcagaactttctacttgtacttgcttatag
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G08120.1 (Glycine max), 5'ss of exon 5
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaattgtggtttgatatattcatgcttgctatatttgtttatccgttttcgggtttattcttttgttggcgttaattaactgtcaagtttaaggt
|| | ||||| || || |||| | ||||||| || | |||||||||||||| ||||||| ||||||||||||||| ||||| |||||||| | | ||| | || | || || | | | | ||| || | ||||| | |||| |
AAAATATTCAAGGGAAAGGATGGTGAGCTCTCTGTTCTGGGAAGACTTGCAGCAGGTGCTTTTGCTGGCATGACATCAACTTTTgtaagtaaattcattgtgacgccccgccttgtatgatttgcagttgctttcattatgttattctgtttcactgcaggggattaaaccttttgttttaaca
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G18140.1 (Glycine max), 5'ss of exon 5
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaatt-gtggtttgatatattcatgcttgctatatttgtttat-ccgttttcgggttt--attcttttgttggcgttaattaactgtcaagt-ttaaggt-----------------------------------------------------------------------
|| | ||||| || | ||| ||||||| || |||||||||||||| ||||||| |||||| |||||||| ||||| |||||||||| || | || | ||| || | ||| |||| | ||| | ||| || | | || | | | | ||| || | || | |
AAAATATTCAAGGGAGAGAATGGCGAGCTCTCTGTTGCAGGAAGACTTGCAGCAGGTGCTTTTGCTGGAATGACATCCACTTTTgtaagtaattcaaggactcatgcttgtatggtttc---attggtttgtgttgttcttatattttgatgcacatatttatataattcagctgacatctctttatatcttgctcatttcttttactaacatgtccaattatccatctatgtatctaatgttgtattatatccatgtag
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA18G42950.1 (Glycine max), 5'ss of exon 6
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaatt-gtggtttgatatattcatgcttgctat-atttgt-------ttatccgttttcgggtttattcttttgttggcgttaattaactgtcaagtttaaggt-----------------------------------------------------------------------
|| | |||| || | ||| ||| || || |||||||||||||| ||||||| |||||| |||||||| ||||| |||||||||| |||| | | ||| || | | |||||| || | || | || |||| | | | | | || | | | | |
AAAATATTCAGGGGAGAGAATGGCAGGCTATCTGTTGCGGGAAGACTTGCAGCAGGTGCTTTTGCTGGAATGACATCCACTTTTgtaagtaattagtggacccttgcttgtatggtttcattgatttgtggtgttcttgtattttgttggtcatatttatgtaatacagctgatatctctttatatcctatatatcttactcatttcttttattaatatccaattatccatctatgtatctaatgttttactatatccatgtag
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA01G28890.1 (Glycine max), 5'ss of exon 3
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaattgtggtttgatatattcatgcttgctatatttgtttatccgttttcgggtttattct--tttgttggcgttaattaactgtcaagtttaaggt-----
|| | ||||| || || |||| | ||||||| || | |||||||||||||| ||| ||| ||||| ||||| ||| ||||| |||||||||| || | || |||| | ||| | | || | ||||| | || ||| | ||||| | ||||||
AAAATATTCAAGGGAAATGATGGTGAGCTCTCTGTTGTGGGAAGACTTGCAGCAGGTACTTTTGCTGACATGATATCAACTTTTGTAAgtaattca---ttatgacgcccagccttgtataacttgcagttgctttcatgatgttattatgtttcattgcaggggattaaaccttttgtttaacaattatg
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv08s0007g02230.t01 (Vitis vinifera), 5'ss of exon 5
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaatt--gtggtttgatatattcatgcttgctatatttgtttatccgttttcgggtttattcttttgttggcgtta-attaactgtcaagtttaaggt
|| | || | || || |||| | ||||||| || || || ||||||||||| |||||||||||||||||||| || ||||| || |||||| | | | | ||| | |||| || |||| | | | | | | ||| | | | || |||
AAACTTTTTAGGGGAAAGGATGGTGAGCTCTCTGTTATTGGTAGACTTGCAGCAGGTGCTTGTGCTGGCATGACGTCCACTTTTgtgagtaatacagcaaacaaaggcgctgaatcttagtttatt-acatactggtttgcaatgtgcctttctaggtggtaatgtggttattgcttggttagca--
upper sequence: AT3G51870.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S91_149V6.1 (Physcomitrella patens), 5'ss of exon 7
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaattgtggtttgatatattcatgcttgctatatttgtttatccgttttcgggtttattcttttgttggcgttaattaactgtcaagtttaaggt------
|| |||||||||||| ||||||| | || ||| | |||| |||||||| || || || |||||||||||||| |||||||||||||| | ||| | | || || | | | | | | | || | | |||||| | || | ||| | | | | || | || |||| |
AAATTGTTCAAAGGTGAAGATGAAGAACTTTCAATTGTCGGTAGACTTGCTGCAGGCGCATGTGCTGGCATGACCTCTACTTTGgtaagca-ttgagctgtg-tagagttgggat--ccacctatgataagttgttttctgaatttgtttttcgggaacctaactt--ttatcttttttattttctcggtMapped 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|19877032|gb|AU237863.1|AU237863EST: TAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTG TTGACATACCCTCTAGATGTTTTGAGAT
genomic: TAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaatt ... tcttatgcagTTGACATACCCTCTAGATGTTTTGAGAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
AACTTGTTCAAAGGTAAAGATGATCAGCTCTCAGTAATCGGAAGACTTGCAGCTGGTGCTTGTGCTGGCATGACATCTACTTTGgtaagtaattgtggtttgatatattcatgcttgctatatttgtttatccgttttcgggtttattcttttgttggcgttaattaactgtcaagtttaaggt
- - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - CAGCTG