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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaataaattttcccggtaggctgtttatgtagtacatattgatttttttttcgatttcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGATGGCAG

Basic information

species Zea mays
transcript GRMZM2G391936_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G391936_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 5
----------gta---aaataaattttcccggtaggctgtttatgtagtacatattgatttttttttcg-atttcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGATGGCAG
          |||   | || | || |    || ||||||| | |||||| || |  |||  ||||  | ||   | || ||||||||||||||||||||||||| ||||||||||||||| ||||| |||||||  ||
gtaattgtctgtacatacatcatttcttgtagttggctgttaaagtagtatatttgaattgattttgggtatccaatttacagAGTCATCGGCAAAGAGGTGCAGACATCAGCATCTGTTGCTTGCCTATTGATGATAG
















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|211493116|gb|FL031298.1|FL031298
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGAT
EST: gi|149101455|gb|EE187574.2|EE187574
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAGGTGCAGGCATCAGCATC
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATC
EST: gi|71429963|gb|DR811013.1|DR811013
EST:     TTCTTTCTGGGGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAA
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAA
EST: gi|71435811|gb|DR816861.1|DR816861
EST:     TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGA
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGA
EST: gi|211114649|gb|FL303211.1|FL303211
EST:     TTCTTTCTG-TGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAG-TGCAGGCATCAGCATC
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATC
EST: gi|211118620|gb|FL303281.1|FL303281
EST:     TTCTTTCTG-TGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAG                         AGTCATCGGCAAAGAG-TGCAGGCATCAGCATC
genomic: TTCTTTCTGGTGACCATCTCTACCGTATGGACTACATGGACTTTGTTCAGgtaaaataaa ... tcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccggtaggctgtttatgtagtacatattgatttttttttcgatttcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGATGGCAG
                         tattgat  putative branch site (score: 3)
                               tttttttttcgatttc  CT-rich tract
            tttatgtagtacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaataaattttcccggtaggctgtttatgtagtacatattgatttttttttcgatttcacttgcagAGTCATCGGCAAAGAGGTGCAGGCATCAGCATCTGTTGTTTGCCAATTGATGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG