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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcttcagttatagtattatcttagatggtatatcaattgatcattgcgtaacttgataatttaaatttctgcatgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g47225.1 (Oryza sativa), 3'ss of exon 10
gtaagttcttcagttatagtattatcttagatggtatatcaattgatcattgcgtaacttgataatttaaatttctgcatgt-cttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG
||||||||| || || |    ||  |  ||||||  ||   |   ||| ||   | | || || || |   |||||   |     |||||||||| ||||||||||| ||| |||||||||||||||| |||||||| ||||||||||| || ||||||
gtaagttctacaattctg---ttgccccagatggcgtacttaa-aatctttagattattttattatatttgtttctttctacatctgcagTCACTGTGCTCATGGGACCCTTGCAAGAGACCAAAGGCTGCAGAAGTTCTCCAGCATACTTTCTTTCAG
















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|60349468|gb|DN216441.1|DN216441
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|32871065|gb|CF010747.1|CF010747
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGC-ATGCAATTGAC-T-ATCTCA                         TCACTATGC-CATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|32932540|gb|CF037352.1|CF037352
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|71304777|gb|DR788504.1|DR788504
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGG
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGG
EST: gi|32832603|gb|CD972281.1|CD972281
EST:     GGCCGACGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: GGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|211496287|gb|FL041699.1|FL041699
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|31350422|gb|CD434779.1|CD434779
EST:     TGGCCGAGGTGATGACCACAGCCAGTAGCGATGCAATTGATCTCATCTCA                         TCACCTATGCTCATGGGATCCTAACAAG
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCAC-TATGCTCATGGGATCCTAGCAAG
EST: gi|32870331|gb|CF010013.1|CF010013
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|32869779|gb|CF009461.1|CF009461
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGATCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|5325074|gb|AI783265.1|AI783265
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|5846886|gb|AI999969.1|AI999969
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCA                         TCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTC
EST: gi|5932684|gb|AW057045.1|AW057045
EST:     TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGATCTCATCTCA                         TCACTATGCTCATGGGATCCTAGC
genomic: TGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGC

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: 306

ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 222

ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 241

ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 247

ATCAAAGGCAGTCAACTGGCCGAGGTGATGACAACAGCCAGTAGCGATGCAATTGACCTCATCTCAgtaagttctt ... tgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatcaattgatcattgcgtaacttgataatttaaatttctgcatgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG
                    taacttgataatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcttcagttatagtattatcttagatggtatatcaattgatcattgcgtaacttgataatttaaatttctgcatgtcttgcagTCACTATGCTCATGGGATCCTAGCAAGAGACCAAAGGCCGCAGAAGTCCTCCAGCATACCTTTTTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT