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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacattttgaggtcattataaggggtatacaaatattgggcttgactttgtttttcgcttgagacaaagcttacctgtttggcctgcatgtgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG

Basic information

species Zea mays
transcript GRMZM2G130034_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130034_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g40550.1 (Oryza sativa), 3'ss of exon 4
-----cacattttgaggtcattataaggggtatacaaatattgggcttg---actttgtttttcgcttgagacaaagcttacctgtttggcctgcatgtgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG
        |||   |   ||||  | |    |    ||  || |   ||     || |||  ||  ||| ||  || |  ||        | ||  ||| ||||||||||||| ||||| |||||||||||||||||||||||||||||||||||| |||||||||||| |||||||||||||||||||||||||
ttaactgtattgccaca-catttgaggaaacagctgaagctttgatatgctaggttggttgctcttttgtgatgaaacaaact-------cttgtttgtatcatacagGTCTGGTTTCCAGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCGGAGGAGCCTACAAGATTTGGAATTAGCTGCTTGGGAAG
















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|148941174|gb|EC886056.2|EC886056
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|71775247|gb|DR973125.1|DR973125
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|78086441|gb|DV514834.1|DV514834
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|148969605|gb|EE020450.2|EE020450
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|213178277|gb|FM185022.1|FM185022
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|31359313|gb|CD443670.1|CD443670
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|76015424|gb|DT942594.1|DT942594
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|50323473|gb|CO518599.1|CO518599
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|91873539|gb|EB403496.1|EB403496
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGGTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|50324880|gb|CO520006.1|CO520006
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|91874398|gb|EB404355.1|EB404355
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAA-GATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|31361617|gb|CD445974.1|CD445974
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|148983478|gb|EE029496.2|EE029496
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|71441173|gb|DR822223.1|DR822223
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|149103753|gb|EE289159.2|EE289159
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|71427278|gb|DR808328.1|DR808328
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|31356201|gb|CD440558.1|CD440558
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|148940595|gb|EC885401.2|EC885401
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|78107618|gb|DV526036.1|DV526036
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
EST: gi|148944452|gb|EC889567.2|EC889567
EST:     GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAG                         GTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA
genomic: GGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGA

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: 45 (upstream exon), 49 (downstream exon)
Score: 75

TTGCAACTGGATCTCATGTTGATGCCATTCCATTCTCAGGCAAATTTGATGGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 96

TTGCAACTGGATCTCATGTTGATGCCATTCCATTCTCAGGCAAATTTGATGGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

TTGCAACTGGATCTCATGTTGATGCCATTCCATTCTCAGGCAAATTTGATGGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 57

TTGCAACTGGATCTCATGTTGATGCCATTCCATTCTCAGGCAAATTTGATGGTGTTGTTGGAGTTCTGGGTGCTCTTGAGGCAATTAGTTTGCTGAAAAGgtaaccgttc ... tgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttgtttttcgcttgagacaaagcttacctgtttggcctgcatgtgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG
                      agcttac  putative branch site (score: 57)
     ttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacattttgaggtcattataaggggtatacaaatattgggcttgactttgtttttcgcttgagacaaagcttacctgtttggcctgcatgtgtcatacagGTCTGCTTTCCTGCCAAAAAGATCTTTGGAGGTTATTATGTTTACATCAGAGGAGCCTACACGATTTGGAATTAGCTGCTTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - atacaaa
- - - - - - - - - - - - - - - - - - -gggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcctgca