Sequence
atgc intronic sequence ATGC exonic sequencegtataaaattgctctcattgtcttgcatttatatttatttgagaaacacatttgctcagaagtgtttttgtccattgttgtttaatcttcttctaaactttctttccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G27410.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 13
gtataaaattgctctcattgtcttgcatttatatttat-ttgagaaacacatttgctcagaagtgttt---ttgtccattgttgtttaatcttcttc----taaactttct--ttccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
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-------------------gttcagcataagctcaaatactatgaaatacgttgttctactactttttgttcttttaattgacgattaaacttgaccatggttattttcctcgtttcagAGTATAGATTCCAAGATTCATCACAACAATCTTATCAACAATATTCTGGCAAAG
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 14
--gtataaaatt-gctctcattgtcttgcatttatatttatttgagaaacacatttgctcagaagtgtttttgtccattgttgtttaatcttcttctaaactttctttccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
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atgaatgagattcattcaaaactaactaaatttctgtttgattgagatactagtgt------aagtttgttcagttgacggtctct--tccttttct----ttgtttaccagAATTTGGATTCAAAGATTCATCACAATAACCTCCTCAATAACATACTTGCAAAG
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 13
gtataaaattgctctcattgtcttgcatttatatttatttgagaaacacatttgctcagaagtgtttttgtccattgttgtttaatcttcttctaa-actttcttt-ccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
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---gagatttgttcaaaccaacaaa-gtatctatttgattggcatgcacctttagtttga------tcaatagact-ttgtcccatccccttttgttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAG
upper sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 23
lower sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 13
gtataaaattgctctcattgtcttgcatttatatttatttgagaaacacatttgctcagaagtgtttttgtccattgttgtttaatcttcttctaa-actttcttt-ccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
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--------ttgttcaaaccaaaaaa-gtatctatttgattggcatacacctttagtttgat-caatataatagact-ttgtcccatccccttttgttgttttctttaccagAATTTGGATTCGAAGATTCATCACAATAACCTTCTCAATAACATACTTGCAAAGMapped 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|116467245|gb|EG509837.1|EG509837EST: ATGGCGGAATTGTGCTGGTGACTGCAACTACACGCCGGAATTCACCCAAC AATTTAGATTCCAAGATTCATCGCAACAACCTCCTCAATAATATACTTGCA
genomic: ATGGCGGAATTGTGCTGGTGACTGCAACTACACGCCGGAATTCACCCAACgtataaaatt ... ttctttccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcagaagtgtttttgtccattgttgtttaatcttcttctaaactttctttccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
ttctaaa putative branch site (score: 2)
tcttcttctaaacttt CT-rich tract
ttgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtataaaattgctctcattgtcttgcatttatatttatttgagaaacacatttgctcagaagtgtttttgtccattgttgtttaatcttcttctaaactttctttccagAATTTAGATTCCAAGATTCATCACAACAACCTCCTCAATAATATACTTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG