Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcgtattgtctgttttccttattatttgcacctcttaagttcatgtgtacctttgatgttatgagtccataatctcttctgatgttgtaaatgagcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12780.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g25320.1 (Oryza sativa), 3'ss of exon 6
gtaagtcgtattgtctgttttccttattatttgcacctcttaagttcatgtgtacctttgatgttatgagtccataatctcttctgatgttgtaaatgag---cagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
| ||| | || | | |||| | | | | ||| | || || | |||| | | | | |||| ||| |||||||||||||| |||||||| |||| |||||| |||||||||||||| ||||| || || ||||||||||||| |||||||| || || |||| || |
----ctactatggggtgaagtgaacacaatttaaa--tttaactttcctaactattattattattatctttttgcagtacttatgctctttgttaatttaattcagGTTCTTTGGCCTGAATGTGGGTGGCGACCTGTATCATTGACTGATTTGATTACAGCCGCATCTGTCAAGAAAGAATACAGGAAAGCAACATTATGCATCC
upper sequence: AT4G12780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os12g36180.1 (Oryza sativa), 3'ss of exon 6
gtaagtcgtattgtctgttttccttattatttgcacctcttaagttcatgt-gtacctttgatgttatgagtccataatctcttctgatgttgtaaatg--agcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
| | | | || || || ||| | ||| || | | | | | || | | | | | ||| | | || ||| | ||||| ||||||||||||||||| ||||||||||| || ||||||| || ||||| ||||| | || || || || || || ||||| || | || ||||
-----tagaaaattgtgaaggactaataatt-actcctattcaacaaacattgcattttagggctagtttgaagagaattattattaattctgttctttctgacagGTACTTTGGCCAGAATGTGGATGGCAACCTGTATCCCTGACTGACTTGATTACTGCTGCTGCGGTTAAAAAGGTATATAGAAAGGCAACATTGTGCATAC
upper sequence: AT4G12780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g43950.1 (Oryza sativa), 3'ss of exon 6
--gtaagtcgtattgtctgttttccttattatttgcacctcttaagttcatgtgtacctttgatgttatgagtccataatctcttctgatgttgtaaatgagcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
| || | || | | || || || ||| | || ||| ||| || | || | ||| | | || || | | | || |||| | | ||| | ||||||||||||||||| |||||| | || || ||||||||||| ||||| | || |||| || || ||||| ||||| || |||| || |
ttgaaaattgtgtcatatgaattgctcatttaattcaatacttcagtacaggc-tat-tctgaaatctttcatctattaatacgt---atcttgtttgtaaacagATACTTTGGCCAGAATGTGGATGGCAAGCAGTATCCTTGACTGATTTGATTACTGGCGCCGCTGTTAAAAAGCAGTACAGAAAGGCAACATTATGCATCC
upper sequence: AT4G12780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G158872_T01 (Zea mays), 3'ss of exon 6
gtaagtcgtattgtctgttttccttattatttgcacctcttaagttcatgtgtacctttgatgttatgagtccataatctcttctgatgt---tgtaaatgagcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
| || | || | | | | | | | | | | | | || | | | | || | | || || | ||| | ||| | ||||||||||||||||| |||||| |||| |||||||||||||||||||| | || |||| ||||| ||||||||||| || || || || |
-----ttacatggaaggtgcttttaaaaaaacggaaataatgaatgccaaattgtctcaaggctcgtaaa-caattccatttactaatatgtatgttctgaaacagATACTTTGGCCAGAATGTGGATGGCAAGCTGTATCATTGACTGATTTAATTACTGGAGCTGCTGTTAAGAAGCAGTACAGGAAGGCAACACTGTGCATTC
upper sequence: AT4G12780.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G839757_T01 (Zea mays), 3'ss of exon 6
---gtaagtcgtattgtctgttttccttattatttgcacctcttaagttcatgtgtacctttgatgttatgagtccataatctcttctgatgttgtaaatgagcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
||| | || | | ||| || | | | | | || | || | | | | |||| || |||| | || | || | ||| ||||||||||||||||||||||| ||||||||||| || | |||||||| ||
ctttaaagacataacctatatttaatttgt-agaagtatttttttaatt-agaagaaatgtcgatgacattctattttaatttgtt----tattctttctgaacagGTTCTTTGGCCAGAATGTGGGTGGCAACCTGTATCCCTCACTGATTTGATC-------------------------------------------------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|125099254|gb|EL155125.1|EL155125EST: CTTTCGACATTACAATAT GTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATT
genomic: CTTTCGACATTACAATATgtaagtcgta ... aaatgagcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgtacctttgatgttatgagtccataatctcttctgatgttgtaaatgagcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
ttctgat putative branch site (score: 3)
ttgtaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcgtattgtctgttttccttattatttgcacctcttaagttcatgtgtacctttgatgttatgagtccataatctcttctgatgttgtaaatgagcagGTTCTTTGGCCAGAATGTGGTTGGCAACCTGTTTCATTGACTGATTTAATTACGGCTGCGTCTGTCAAGAAAGTTTACAGGAAGGCCACTCTATGTATAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA