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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaacagttatatgattaccaacttaattaatgtgctttcgactttatatgctatatgcacgatgtactgagctgggactcttttactttaattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC

Basic information

species Zea mays
transcript GRMZM2G119725_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g19510.1 (Oryza sativa), 3'ss of exon 12
------tcaacagttatatgattaccaacttaattaatgtgctttcgactttatatgctatatgcacgatgtactgagctgggactcttttacttta------attatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC
      ||  |  | |||| |||  | ||||    ||||   || | | |           || || |    ||||||||   || ||| |  ||||      ||||  ||||| ||||||||||| |||||||| || |||||||||||||||||||||||| | || || |||||||| ||||||                         
ttgtgctccgccttcatatcattttccacttcg--aatgctattccaaatc----------atccatggatcactgagcttaaacacttctgttttacatgaaattaatcagCCTGCTCATGAGAAGATTGGAGTCGTCGATGCTCAATGGATTGTTCATCAAGCTGTGCCATCACTTGGAAACCAG-------------------------

upper sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA13G39990.1 (Glycine max), 3'ss of exon 12
tcaacagttatatgattaccaacttaattaatgtgctttcgac-tttatatgctatatgcacgatgtactgagctgggactcttttactttaat---tatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC
     |  ||  | | ||  || |       ||   | ||     ||| ||   || | |         |||  |       ||| | || |||   | | ||||| || ||||| |||||||| ||  ||||| | ||||||||||||||||||  | ||||||| ||||| ||||||                         
---gtaaata-gtaaatagtaaatatgggggtgcaatctcattacttaaataaaatcttctaagcaatttgatttacttagttttaatttgaatccttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------

upper sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA12G29800.1 (Glycine max), 3'ss of exon 12
----tcaacagttatatgattaccaacttaattaatgtgctttcgactttatatgctatatg-cacgatgtactgagctgggactcttttactttaattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC
      |  |  |||  || ||| | || | |  |  |   |   |  || || |  || ||      | || | ||||   |   ||| | ||   || | ||||| || ||||| |||||||| ||  ||||| | ||||||||||||||||||  | ||||||| ||||| ||||||                         
gtaaatagtaaatatgggagtacgatctcatt--acttaaataaaatcttctacgtaatttggtttagtttatttagctttaa---tttgaattcttttttgcagCCAGCACATGAAAAAATTGGTGTAATTGATTCACAATGGATTGTTCATCAAGTAATTCCTTCTCTTGGGAACCAG-------------------------

upper sequence: GRMZM2G119725_T01 (Zea mays), 3'ss of exon 12
lower sequence: PP1S448_20V6.3 (Physcomitrella patens), 3'ss of exon 12
------------------tcaacagttatatga-ttacca--acttaattaatgtgcttt--cgactttatatgctatatgcacgatgtactgagctgggactcttttactttaattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC
                  ||||   |  ||||| |||  |     |||  | |  ||| |  ||   || |      |    |   |   ||   ||    | | |  | |||    |||||||| ||||| |||||||||||||| |||||||    ||||||| | ||       || || |||||||| || |||                         
gtaactctgcttccgaactcaagtttgttatgagttaatattgtataaacagtcagctattgcggaattctgattagtgaatattctccgctcttcttaagcgcatc-attttgtccatacagCCTGCTCACGAGAAAATTGGAGTAGTTGATGAAACATGGATTATACACGTCGGTGTACCATCACTTGGAAATCAG-------------------------

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|211026567|gb|FL468579.1|FL468579
EST:     ACTTGGTCCATGGATNGGGTCTTGAC-TTGCTCTTAGAAAATGTGTGGAS                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|148928292|gb|EE284900.2|EE284900
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|16927462|gb|BM080531.1|BM080531
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|60338690|gb|DN205663.1|DN205663
EST:     TGACTTTGCTCTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: TGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|74234754|gb|DT642668.1|DT642668
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGTTCTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|71427884|gb|DR808934.1|DR808934
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|78073793|gb|DV502227.1|DV502227
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTTTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|74234755|gb|DT642669.1|DT642669
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
EST: gi|149108357|gb|EE292695.2|EE292695
EST:     ACTTGGTCCATGGATGGGGTCTTGACTTTGTTCTTAGAAAATGTGTGGAG                         CCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA
genomic: ACTTGGTCCATGGATGGGGTCTTGACTTTGCTCTTAGAAAATGTGTGGAGgtattccctg ... aattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgctatatgcacgatgtactgagctgggactcttttactttaattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC
                                         ctttaat  putative branch site (score: 4)
                                  tcttttactttaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaacagttatatgattaccaacttaattaatgtgctttcgactttatatgctatatgcacgatgtactgagctgggactcttttactttaattatacagCCGGCTCATGAGAAAATTGGAGTTGTTGATGCTCAATGGATTGTTCATCAATCAGTTCCTTCACTTGGCAACCAGGGCAAGTCAGATAATGGAAGACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - -tgctttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -atgcacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctggg