Sequence
atgc intronic sequence ATGC exonic sequenceCTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G05580.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os07g49310.2 (Oryza sativa), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagt-attcatgttgtttaccttgcag
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CTGCCGCCGCCGCGCGCCTCCACAGCTGCCTCGCCTGGCCGCTCTACTGGGCGGCGCAGGGAACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtacga--cggtattcat-ttccattt--tgattcc---tactccactctactacactagtagtaattaattcgttcatggaattggaattgcag
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G128971_T01 (Zea mays), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtat-caactaatcctc-atgcttcatctgcctacttcaagtgttttgatctctctcta--tattgttaaccaagta---ttcatgttgtttac-cttgcag------------------
| || | || || | || ||| ||||| ||||||| ||||||||| ||| || || |||||||||||||| ||||| ||||| ||||| |||||||| | | | |||| | | | | || || | | | | | | | || |||| | | || | || | | || || | ||| |
CCGCAGCGGCCGCGCGCCTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtaggcctccagccctccacggtcccgtgcccaacattggatactcttttttttgtcctgttattttcattcatgccagttttaggcctttgactcctgctgcatatctgctgtttgcag
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G074401_T01 (Zea mays), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtatt-catgttgtttaccttgcag
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CCGCGGCCGCCGCGCGCCTCGACAGCTGGCTCGTCTGGCCGCTCTACTGGGCCGCGCAGGGCACCATGTTCTGGGCGCTCTTCGTCCTCGGCCACGACTGgtacgcaccaatgttctggattgccctgttgttgtttttcatggaagctttggactctggtctttgacttgtgccgcatgtctgctgt-ttgcag
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv13s0067g01120.t01 (Vitis vinifera), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag
| |||| || ||||| |||||| ||||| | | |||||||| |||||||||||||| || ||||||||||||||||||||||| ||||| ||||||||||| | || || | ||| || | ||| | | | | || | ||| | || |||| | | | || | | | |||
CGGCTGCAGCGGCTTATTTCAACCATTGGGCTGTTTGGCCTCTGTACTGGTTCGCTCAGGGGACCATGTTCTGGGCTCTCTTTGTTCTTGGTCATGACTGgta---atctattttctt-cttgattttcctgtt--gaatttcaagacccaattctctgtttttaatgggattgtgttattctggattgtacag
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S98_209V6.1 (Physcomitrella patens), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgta--tcaactaatcctcatgcttcatc---tgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag--
| |||| ||||| || |||| ||| || | ||||| | |||||| | || |||||||||||||||||||||||||| || || || || |||||||| | ||||| | | | || || | || | ||| | || | | | | | | || | | || | |
CGGCTGGCGCTGCAGCTTTGAACAGCTGGTTTGTTTGGCCGTTGTACTGGCTGGCACAAGGAACCATGTTCTGGGCTCTCTTCGTGCTGGGTCACGACTGgtaattgcactaaaacctgttcgagattgagtgaatgtttaatttgtgtgaggctgtgtggacaattccatgtgag-agacgtggaatcctgtgagtgctt
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S65_6V6.1 (Physcomitrella patens), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgta--tcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag----
| || | ||||| | |||| ||| || | ||||| | |||||| | || |||||||||||||| ||||||||||| || || |||||||||||||| | |||| || | | || | ||| | | | ||||| | | | || | || ||
CCGCCGGCGCTGCAGCTGTGAACAGCTGGTTTGTGTGGCCGTTGTACTGGCTGGCGCAAGGAACCATGTTTTGGGCTCTCTTCGTGCTGGGCCATGACTGgtaattgtactataacttgttcgagattgagaggacacgcaattttcgtgagaatgcgggaatgttagatgtggaattctgagagtagccagacatgcca
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ23113 (Selaginella moellendorffii), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag
|||||| |||||||||||| || |||||||| ||||||| ||||||||| || ||||| || |||||||||||||||||||| || |||||||||||||| | | || || || | | || || ||| | | | || | ||
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGGACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgta--agtttttcttc---tcccaaaaacttgtttt---tgctttctcgttcttacgcgtctttgatcag------------------------
upper sequence: AT5G05580.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ20170 (Selaginella moellendorffii), 5'ss of exon 1
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag
|||||| |||||||||||| || |||||||| ||||||| ||||||||| || ||||| || |||||||||||||||||||| || |||||||||||||| | | | | || | | || | | | ||||| | | || | ||
CTGCTGGTGCTGCTTACTTGAATAATTGGCTCGTCTGGCCACTCTACTGGGCTGCCCAAGGCACGATGTTCTGGGCTCTCTTTGTGCTCGGCCATGACTGgta------agtttttctctcccagcaa--tgttttttctttctcgatcttac---gcgtctttgatcag------------------------Mapped 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|125178697|gb|EL197001.1|EL197001EST: CCTTGGCCATGACTG CGGACATGGTAGCTTCTCGAATGATCCGAGGCTGAACAGTGTGGCTAGGTC
genomic: CCTTGGCCATGACTGgtatcaacta ... taccttgcagCGGACATGGTAGCTTCTCGAATGATCCGAGGCTGAACAGTGTGGCT-GGTC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CTGCTGTTGCTGCTTACTTCAACAATTGGCTTCTCTGGCCTCTCTACTGGTTCGCTCAAGGAACCATGTTCTGGGCTCTCTTTGTCCTTGGCCATGACTGgtatcaactaatcctcatgcttcatctgcctacttcaagtgttttgatctctctctatattgttaaccaagtattcatgttgtttaccttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA