Sequence
atgc intronic sequence ATGC exonic sequence...tggtgaaagtttgatacttggtttggtaaatatagaatgaggaattcggtatcatttctgatgagctacgtcatgacagtgctgtgatttgtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G13850.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 2
--tggtgaaagtttgatacttggtttggtaaatatagaatgaggaattcggtatcatttctgatgagctacgtcatga-cagtgctgtgatttgtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGT
|| | || | ||| || | | | || | | | ||| | || | || | | | | || ||| |||| | ||||||| || ||||| ||| | ||| ||||||||||||||| |||||||| ||||| || ||||| ||| |||||||||| ||||| || |||||||||||
taacctgcaccctttgaatttg--ctgtctgtttttatctctggtgtgtgaaacaattgcagacctg-tatctgacaagtattggtgtcattttcatcttcagGACAAGAAGGGGATGCCAGCGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGT
upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 2
-------tggtgaaagtttgatacttggtttggtaaatatagaatgaggaattcggtatcatttctgatgagctacgtcatgacagtgctgtgatttgtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGT------
| | | |||| | || ||| || | | | ||| | || || | |||| || || | | || | | || | |||| || ||||| ||| ||||| ||||||||||||||| |||||||| ||||| || || || ||| |||||||||| ||||| || |||||||||||
tcctgtgcgctttgaatttgctgtctgtttt--tatctctggtatgtgaaaca-attacaacacctgacaag-tat-ttgtctcattttcatctttcgc--------gacaagAAGGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCG
upper sequence: AT5G13850.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
----tggtgaaagtttgatacttggtttggtaaatatagaatgaggaattcggtatcatttctgatgagctacgtcatgacagtgctgtgatttgtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGT---------
| | | |||| | || ||| || | | | ||| | || || | |||| || || | | || | | || | |||| || ||||| ||| ||||| ||||||||||||||| |||||||| ||||| || || || ||| |||||||||| ||||| || |||||||||||
tgtgcgctttgaatttgctgtctgtttt--tatctctggtatgtgaaaca-attacaacacctgacaag-tat-ttgtctcattttcatctttcgc--------gacaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGTMapped 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|125055864|gb|EL125861.1|EL125861EST: GATGACAATGATGAGGATGATTCCGAGGACGATGACGAGGCGGAGG GACATGATGGGGAGGCCGGTGGCCGGT
genomic: GATGACAATGATGAGGATGATTCCGAGGACGATGACGAGGCGGAGGgtaagttttt ... gtttaaccagGACATGATGGGGAGGCCGGTGGCCGGT
EST:
gi|164031524|gb|ES005105.1|ES005105EST: GATGAGGATGATTCCGAGGACGATGACGAGGCGGAGG GACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAA
genomic: GATGAGGATGATTCCGAGGACGATGACGAGGCGGAGGgtaagttttt ... gtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAA
EST:
gi|124862242|gb|EH946679.1|EH946679EST: ATGATGACAATGATGAGGATGATTCCGAGGACGATGACGAGGCGGAGG GACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTG
genomic: ATGATGACAATGATGAGGATGATTCCGAGGACGATGACGAGGCGGAGGgtaagttttt ... gtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcggtatcatttctgatgagctacgtcatgacagtgctgtgatttgtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGT
ttctgat putative branch site (score: 3)
tttgttt putative PPT
atttgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggtgaaagtttgatacttggtttggtaaatatagaatgaggaattcggtatcatttctgatgagctacgtcatgacagtgctgtgatttgtttaaccagGACATGATGGGGAGGCCGGTGGCCGGTCAAAGCAAAGCAGAAGTGAGAAAAAGAGTCGTAAAGCTATGTTGAAGCTTGGGATGAAACCAATCACTGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - -agtttga
- - - - - - - - - -ggtttgg