Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAGCTAAAGTAGTAGCTGCAATGCTAATGTTTGCGACAGTATGTGGTATCTT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G16780.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G069410_T01 (Zea mays), 3'ss of exon 5
gtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAGCTAAAGTAGTAGCTGCAATGCTAATGTTTGCGACAGTATGTGGTATCTT
||||||| ||| ||| | | ||| | || | || || | || | || | || |||| |||| |||||||| ||||| |||||||||| || ||| | |||||||||||||| ||||| | ||||| ||||||||||| || ||| || |
gtgagtct-------tgtaggtcatatctgtg----gtgactggcactcg-atgcttttctaatttggtttacgcg--gtttgcagGCGTTGTCTTCCGGATTTTGGGCCACTACACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTGATGTTTGCGACGGTCGCTGGGATTCT
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: GRMZM2G075900_T01 (Zea mays), 3'ss of exon 13
gtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAGCTAAAGTAGTAGCTGCAATGCTAATGTTTGCGACAGTATGTGGTATCTT
||||||| ||| || | | ||| || | | || | | | || ||| || ||| |||| |||| |||||||| ||||| ||| |||||| || ||| | |||||||||||||| ||||| | ||||| ||||||||||| || |||||| |
gtgagtct-------tgtaggccatgtttgtgg--tgactagcactca-atgtgcttttctaatttgaattatgtg--gtctgcagGCGTTGTCTTCCGGATTTTGGGCCACTCCACTGGTCAGCCTCTTCTTGGAGCTAAAGTTGTAGCCTCCATGCTTATGTTTGCGACGGTTGCTGGTATTCT
upper sequence: AT1G16780.1 (Arabidopsis thaliana), 3'ss of exon 14
lower sequence: Vv09s0054g00700.t01 (Vitis vinifera), 3'ss of exon 13
---------------gtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtcc---acagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAGCTAAAGTAGTAGCTGCAATGCTAATGTTTGCGACAGTATGTGGTATCTT
|||| | ||| | || | || | | | | | || | | | ||| || ||| |||| ||| |||||||||| |||||||||||||| ||||| ||| | || || |||||||| || ||| ||||| | |||||||| ||||| ||||| |
aaccttcaaccttttgtgattgagtgatcttgctattttcgtttcttgtttcgttcggttat---tttggggctttctcatcttatgttt-atatcccttgcagGCTTTCTGTTCCGGATTTTGGGATACTACACCGGACATCCTCTACTCGGGGCTAAAGTTGTGGCTTCAATGTTGATGTTTGCAACAGTTGCGGGTATACTMapped 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|124825050|gb|EH909916.1|EH909916EST: TCACCCATTGCAGTTG GTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAG
genomic: TCACCCATTGCAGTTGgtgagtcagt ... atgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAGCTAAAGTAGTAGCTGCAATGCTAATGTTTGCGACAGTATGTGGTATCTT
atttgat putative branch site (score: 5)
tatttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcagtaaaaatgttggttaagcccgtgaaacgagaaagaaacagacataaggaaccaacgctctctatttgatgtccacagGTTTTGTGTTCCGGATCTTGGGATACTACACTGGACAACCTTTGCTTGGAGCTAAAGTAGTAGCTGCAATGCTAATGTTTGCGACAGTATGTGGTATCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC