Sequence
atgc intronic sequence ATGC exonic sequence...atttagttaatagtgaatggattcttatgattggtcacaaacctttgttgtgttctttccataaggactcttttcaaacttcgtgctttatgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G53140.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os05g50970.1 (Oryza sativa), 3'ss of exon 5
---atttagttaatagtgaatgg-attcttatgattggt--cacaaacctttgttgtgttcttt-----------ccataaggactcttttcaaacttcgtgctt---tatgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG
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gtgcttctgtttacaaaagatgttgttcatttatttaatactggatgcagttgttgcattctttgtggcggtgtacctgctgaattgttgttaaacatttcgtttccctcctatttatagCTATTGCACTCTCTGAGGATCACAAGCCAAATAGAAGCGATGAGAGGAAGCGAATTGAGAGTGCTGGTGGGGTTGTTATGTGGGCTG
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G412937_T01 (Zea mays), 3'ss of exon 5
-atttagttaatagtgaatggattcttatgattggtcacaaacctttgttgtgttctttccataaggactcttttcaaacttcgtgct--ttatgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG
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cattaggatatctgt-attgctgtggcaggtcttgtctgtaatcca-gatgtag-ctgtctgttgaactgtttgtaaaacatcatgttgcctctattttgcagCTATTGCGCTCTCTGAAGATCACAAGCCAAACAGAAGTGATGAGAGGAATCGAATTGAGAGTGCTGGTGGGATAGTTATGTGGGCAG
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 5
--atttagttaatagtg-aatggattcttatgattggtcacaaacctttgttgtgttctttccataaggactcttttcaaacttcgtgctttatgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG
|| | | | || |||| | | || || ||| | || | ||||| | | | | || | ||| | ||| ||||| || || || ||||| || ||||||||||||||||| ||||| | ||| ||||||| | ||||||||||||| ||||||||||||
gtccttgtctggtcatatgatagattttctactatagttcca---cttgaatacattttagaaataagaatgatatcttgaattaattttttttttttggcagCAATTGCTCTCTCTGAGGATCATAAGCCAAATAGAAGTGATGAGCGGAAGAGAATTGAGAATGCTGGTGGTGTTGTCATGTGGGCAG
upper sequence: AT5G53140.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 6
-atttagttaatagtg-aatggattcttatgattggtcacaaacctttgttgtgttctttccataaggactcttttcaaacttcgtgctttatgttttg-cagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG
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tccttgtctggtcatatgataaattttctcctacagttcca---tttgaatacattttggaaataagattggtatcttgaattaattttttttattttggcagCAAATGCTCTCTCTGAGGATCATAAACCAAATAGAAGTGATGAGCGGAAGAGAATCGAGAATGCTGGTGGTGTTGTCATGTGGGCAGMapped 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|116416941|gb|EG459533.1|EG459533EST: TGTTGCAAATGTTGGAGACTCGAGGACAATAGTTTCTAAAGCTGGGAAAG CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGC
genomic: TGTTGCAAATGTTGGAGACTCGAGGACAATAGTTTCTAAAGCTGGGAAAGgtcagtatgt ... tgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGC
EST:
gi|164146193|gb|ES020760.1|ES020760EST: TGTTGCAAATGTTGGAGACTCGAGGACAATAGTTTCTAAAGCTGGGAAAG CGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAG
genomic: TGTTGCAAATGTTGGAGACTCGAGGACAATAGTTTCTAAAGCTGGGAAAGgtcagtatgt ... tgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgtgttctttccataaggactcttttcaaacttcgtgctttatgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG
tttatgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttagttaatagtgaatggattcttatgattggtcacaaacctttgttgtgttctttccataaggactcttttcaaacttcgtgctttatgttttgcagCGATCGCGCTATCTGATGACCATAAGCCAAATAGAAGCGATGAAAGAAAGCGAATTGAAAGTGCTGGTGGTGTTATCATGTGGGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - -cacaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcaaact