Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttagatcttccattatttcttttcatattttattttcaaaatctatacatcttcgttttacatttctcaccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCATCGACGATAATGCCCCACATGATCAG

Basic information

species Arabidopsis thaliana
transcript AT5G64500.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G64500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 3
gtaagtgtttagatctt-----ccattatttctt--ttcatattttattttcaaaatctatacatcttcgtt--------ttacatttctca------ccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCATCGACGATAATGCCCCACATGATCAG
||||||   | |   ||       || | ||| |  |||| || |  |  | |||||  ||    ||  | |          ||| |||||         ||| | ||||| |||||||||||||| ||||||||| |||||||||| || |||||||| || |||||||| |||   |  |||
gtaagtaccttgtcattgtgaataatcaattcatgtttcagatctgttacttaaaataaatcttactctgataatgacacgaacaattctccaattattgttacttagGTTAGTTGGTGTTGGTGAAGCATCATTTATAAGTCTTGCAGCTCCATTCATTGATGATAATGCTCCAGCAGCACAG

upper sequence: AT5G64500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G30370.1 (Glycine max), 3'ss of exon 4
----------------------gtaagtgtttagatcttccattatttcttttcatattttat--tttcaaaatctat-acatcttcgttt-----tacatttctcaccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCATCGACGATAATGCCCCACATGATCAG
                        || | | | | | |  ||||   |     |||| |  ||  | | | || || | | || ||  |||     |||  || |    |||| |||| | ||||||||||||||||| |||||| |||||||||| || || ||||| || || |||||||||  |   |||
gtaagtgtcttcagttatttattgaactctatggttttggcattgaatacaaacatagtacatgatgtaagaacctgtcatatttttttttccttatactgttgtatttttatacagGCTAGTTGGTGTTGGTGAGGCTTCATTTATAAGTCTTGCAGCACCTTTCATTGATGACAATGCCCCAGTTTCACAG

upper sequence: AT5G64500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G06880.1 (Glycine max), 3'ss of exon 4
----------------------gtaagtgtttagatcttccattatttcttttcatattttat--tttcaaaatctatacatc---ttcgttttacatttctcaccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCATCGACGATAATGCCCCACATGATCAG
                        || | | | | | || ||||   |   |||||| |  ||  | | | |||||  | ||    ||| || |||  || |    || | |||| | ||||||||||||||||| |||||| | |||||||| || || ||||| || || |||||||||  |   |||
gtaagtgtcttcagttatttattgaactctatggtttttgcattgaatacattcatagtacatgatgtaagaatcttcatatttttttccttatactgttgtatttttctacagGCTAGTTGGTGTTGGTGAGGCTTCATTTATGAGTCTTGCAGCACCTTTCATTGATGACAATGCCCCAGTTTCACAG

upper sequence: AT5G64500.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0282g00040.t01 (Vitis vinifera), 3'ss of exon 1
gtaagt-gtttagatcttccattatttcttttcatattttattttcaaaatctatacatct-------tcgttt---tacatttctcaccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCATCGACGATAATGCCCCACATGATCAG
|||||| |  ||  |   | | | |    | ||   ||      | | ||| | ||  |||       | |||    | | ||| |||     || ||||||||||||||||||||||| |||||| ||||||||||||| |||||||| || || |||||||||  || ||||
gtaagttgcctaattgcactactttaaaatgtccacttacgacataagaatttgtatgtctgtttcagtagttaaaatgcttttatcattccttttagGTTTGTTGGTGTTGGTGAGGCTTCATTTATAAGTCTTGCTGCTCCATTCATTGATGACAATGCCCCAGTTGCTCAG

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|116476814|gb|EG519406.1|EG519406
EST:     ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCAT                         GTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCAT
genomic: ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCATgtaagtgttt ... ccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCAT
EST: gi|124704880|gb|EH796282.1|EH796282
EST:     ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCAT                         GTTTGTTGGTGTTGGTGAGGCA
genomic: ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCATgtaagtgttt ... ccttattcagGTTTGTTGGTGTTGGTGAGGCA
EST: gi|124965151|gb|EL039360.1|EL039360
EST:     ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCAT                         GTTTGTTGGTGTTGGTG
genomic: ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCATgtaagtgttt ... ccttattcagGTTTGTTGGTGTTGGTG
EST: gi|164178982|gb|ES133641.1|ES133641
EST:     TTTTGGTCCATCACAATCTGTCGCAT                         GTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCAT
genomic: TTTTGGTCCATCACAATCTGTCGCATgtaagtgttt ... ccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCAT
EST: gi|125165420|gb|EL191710.1|EL191710
EST:     ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCAT                         GTTTGTTGGTGTTGGTGAGGCATCA
genomic: ATTGGCTGCGGTCTTTCGTTTGATTTTTGGTCCATCACAATCTGTCGCATgtaagtgttt ... ccttattcagGTTTGTTGGTGTTGGTGAGGCATCA
EST: gi|164215022|gb|ES054763.1|ES054763
EST:     ATCTGTCGCAT                         GTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCAT
genomic: ATCTGTCGCATgtaagtgttt ... ccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCAT
EST: gi|164045616|gb|ES010901.1|ES010901
EST:     TTTTGGTCCATCACAATCTGTCGCATT                         GTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCA
genomic: TTTTGGTCCATCACAATCTGTCGCA-Tgtaagtgttt ... ccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttattttcaaaatctatacatcttcgttttacatttctcaccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCATCGACGATAATGCCCCACATGATCAG
                                       ttctcac  putative branch site (score: 2)
                                      tttctcaccttattc  CT-rich tract
     ttattttcaaaatcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtttagatcttccattatttcttttcatattttattttcaaaatctatacatcttcgttttacatttctcaccttattcagGTTTGTTGGTGTTGGTGAGGCATCATTTGTAAGTCTTGCTGCCCCATTCATCGACGATAATGCCCCACATGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC