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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtccatattttataatttggtgtcacaatatcttagttcatagttaatctgaatctgatagtcagttcattcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG

Basic information

species Zea mays
transcript GRMZM2G151916_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151916_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g14130.1 (Oryza sativa), 3'ss of exon 5
gtatgtccatattttataatttggtgtcacaatatctta--gttcatagttaatctgaat-----ctgatagtcagttcat-----tcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG
|||||| |||  || |    ||| | |   |||| | |   ||| | |||  ||||||||     |||||  | | || ||     |  | |||||| |||||  | ||||||||||| || ||||||||||||||||| || |||||||||
gtatgttcat--ttcacg-cttgatattttaataacctgtggttaacagt--atctgaatataagctgattcttactttatattggttttaatagGTCGATCCTCTTACTCACCAAGTCAAAATATGTGATTTTGGGAGCGCAAAAATGTTG
















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|32908149|gb|CF012962.1|CF012962
EST:     ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTCGGGAGTGCCAAA
genomic: ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|60398307|gb|DN231123.1|DN231123
EST:     ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTG                         GTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|211015494|gb|FL335940.1|FL335940
EST:     CACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTCGGGAGTGCCAAA
genomic: CACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|211033507|gb|FL333369.1|FL333369
EST:     ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTG                         GTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|91875587|gb|EB405544.1|EB405544
EST:     ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTG                         GTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|32845700|gb|CD985381.1|CD985381
EST:     ACCTGGTGTTTGCCACAGGGATGTGAAACCACAAAATCTTTTG                         GTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTCGGGAGTGCCAAA
genomic: ACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
EST: gi|211159258|gb|FL355922.1|FL355922
EST:     ACACAGTACCTGGTGTTTGTCACAGGGATGTGAAACCACAGAATCTTTTG                         GTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA
genomic: ACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

ATATTTCGAGGTTTAGCCTATATTCACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 168

ATATTTCGAGGTTTAGCCTATATTCACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 159

ATATTTCGAGGTTTAGCCTATATTCACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

ATATTTCGAGGTTTAGCCTATATTCACACAGTACCTGGTGTTTGCCACAGGGATGTGAAACCACAGAATCTTTTGgtatgtccat ... ttcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatatcttagttcatagttaatctgaatctgatagtcagttcattcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG
                            atctgat  putative branch site (score: 146)
                                         ttcattc  putative PPT
                                            attcattata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtccatattttataatttggtgtcacaatatcttagttcatagttaatctgaatctgatagtcagttcattcattatagGTTGATCCATTGACTCACCAAGTGAAGATATGTGATTTTGGGAGTGCCAAAATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA