Sequence
atgc intronic sequence ATGC exonic sequencegtttaccttgaatctttgatgtttgcataaatttctcattcacttgttattgtagatattgacactgttctcctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25490.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os09g07510.1 (Oryza sativa), 3'ss of exon 9
-------------gtttaccttgaatctttgatgtt---tgcataaatt-tctcattcacttgttattgtagatattgaca--ctgttctcctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
| || | | ||| ||| || | || | | | | || || |||| |||| || | | ||| || |||||| ||| ||| | || ||||| ||||||||| | |||||||| || |||||||||||||| |||||||| |||||||| || | || |||
ttgtgttcagtgattatatagtttttttttaatgcagaatggacaagtggtatttataacctgctatttaagatgtttttaactggatctttaattttagGTCTTCTCAATCAGAGATGCTGCTGCAAACAACTTGAAGCGCCTAGCTGAGGAGTTTGGTCCAGAATGGGCGATGCAGCATATAATCCCTCAG
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G164352_T04 (Zea mays), 3'ss of exon 9
--------------------------------------------------------gtttaccttgaatctttga-tgtttgcataaatttctcattcacttgttattgtagatattgacactgttc-----tcctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
|||| ||| ||| |||| || | | ||| | || | | || | | | | ||| | ||||||||| || ||| | || ||||| || |||||| | |||||||| ||||| ||||||||||| || |||||||||||||| || | || |||
gtttgtatcattagggttatgtcaaaacagtatctctttggagctgtctccagcgtctttatcttatatccttgagtgcatattggactttgtaatgtattgactaaaattgtcagtttaactaactaaaatttggatttcagGTCTTTTCAATCAGAGATGCTGCCGCTAACAACTTGAAGCGCCTTGCAGAAGAGTTTGGTCCAGAGTGGGCAATGCAGCATATAATCCCTCAG
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G122135_T04 (Zea mays), 3'ss of exon 9
--------------------------------------------------------------gtttaccttgaatctttga-tgtttgcataaatttctcattcacttgttattg---tagat--attgacactgttctcctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
| | |||| ||| | || || | | | || | || | | || || ||||| | | || | | ||||||||| ||| ||| | || ||||| || |||||| | |||||||| || || ||||| ||||| || |||||||||||||| || |||| |||
gttcgtatcactagacttatgtcaaaacagtaacgctgtggggctactcaagcatctttcctttccatcttgtatcctcgagtgcatataggacattgtgatgtattgactaatggtttagattaactaac-caaaatttggatttcagGTCTTCTCAATCAGAGATGCTGCCGCCAACAACTTGAAGCGCCTTGCGGAAGAGTTCGGTCCAGAGTGGGCAATGCAGCATATAATTCCTCAG
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 8
------------gtttaccttgaatctttgatgtttgcataaatttctcattcacttgttattgtagat----attgacac-tgttctcctcctt--cagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
| || | | | | | || || | | | |||| | | || ||||| | | |||| | || || | | ||||| ||||| || || || ||||| || |||||| |||||||||| ||||| || ||||||||||| |||||||||||||||||| |||| |||
tattttaagagggctttcatcatctttgtcatcgttttctttgtctgtcatctatgtatttatgtagttcaaaagggacaaatattatcatgttgtgcagGTTTACTCCATTCGTGATGCTGCTGCTAACAACTTAAAGCGCCTTGCAGAAGAATTTGGTCCTGACTGGGCAATGCAGCACTTAATTCCACAG
upper sequence: AT1G25490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: PP1S214_34V6.1 (Physcomitrella patens), 3'ss of exon 8
--------------------------------------------------gtttaccttgaatctttgatgtttgcataaatttctcattc--acttgttattgtagatattgacactgttctcctcctt--cagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
| | | | |||| | ||| |||| | || || ||| ||| | ||| | || | || | || |||| ||||||||||| || || || || ||||| || ||||| || || || |||||||||||||| |||||| |||||||| | |||| |||
gttcatatattcccatcaagcaatgtttcgatggtggtttgtgtcgagatggtcgtcctcaatcagatctcttttcatatttgcttctttagaactagttcagtaatataatttcattcttttttggattaatagGTGTACTCTATCCGAGAGGCAGCTGCCAACAATCTCAAGCGTCTTGCCGAAGAGTTTGGTCCTGAGTGGGCATTGCAGCACATCATTCCACAGMapped 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|124720349|gb|EH811751.1|EH811751EST: CGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAG GTCTACTCTATCCGCG
genomic: CGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAGgtttaccttg ... cctccttcagGTCTACTCTATCCGCG
EST:
gi|125115287|gb|EL165345.1|EL165345EST: TTTTCGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAG GTCTACTCTATCCGCGAAGCTGCAG
genomic: TTTTCGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAGgtttaccttg ... cctccttcagGTCTACTCTATCCGCGAAGCTGCAG
EST:
gi|47830292|gb|CK119976.1|CK119976EST: TTTTCGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAG GTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAG
genomic: TTTTCGATGACAAGCTCGGAGCCCTTTGCATGCAATGGCTGCAAGACAAGgtttaccttg ... cctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataaatttctcattcacttgttattgtagatattgacactgttctcctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
tattgac putative branch site (score: 2)
cactgttctcctcctt CT-rich tract
ttattgtagatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttaccttgaatctttgatgtttgcataaatttctcattcacttgttattgtagatattgacactgttctcctccttcagGTCTACTCTATCCGCGAAGCTGCAGCAAACAACCTAAAGCGCCTCGCAGAGGAGTTTGGTCCTGAATGGGCAATGCAGCACTTAGTTCCCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG