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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgtggactgccagcttgacaaatgttatttggctggaaaaattaagagtaaattccggatcaatttgatggtgctaatatattattttcaacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA

Basic information

species Zea mays
transcript GRMZM2G092129_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092129_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os07g22640.3 (Oryza sativa), 3'ss of exon 4
------tcgtggactgccagcttgacaaatgttat-ttggctggaaaaattaagagtaaattccggatcaatttgatggtgctaatatattattttcaacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA
      |   | |     |      ||  || ||| || ||| |   |   ||     | ||  || |     ||||||| || | || ||  |||       |||||| |  || ||||| ||| |||||||||| ||| ||||||||||||||   |||||   ||| || |||||||| ||||| || |||||||||||| | |
tgtgcatttcgtaaaaaaaatggtgcatttggtatgtttgctagtttaggaaaataatatttgtggttgtgcatgatggttctgacattttgcttt-------tcagGTCACATATCACCCATTTTCAAAGGAAGAACAGATGGAAGCCCTAGAGTCTGAAAAGAGAGCTATCGAGGAGAGAAAGCGACTCAAGGAGGCTGGGGTTA
















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|37375612|gb|CF624255.1|CF624255
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGTACCACCCCTTTACCAAAGGAAGAGCAGCTGGAAGCCCTAGAGAT
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTA-CAAAGGAAGAGCAGCTGGAAGCCCTAGAGAT
EST: gi|7162378|gb|AW520000.1|AW520000
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGNACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
EST: gi|78025647|gb|DV494034.1|DV494034
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
EST: gi|148971558|gb|EE022271.2|EE022271
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
EST: gi|6721070|gb|AW308707.1|AW308707
EST:     TTACATCTTAAG                         GTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: TTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
EST: gi|67025946|gb|CO454695.1|CO454695
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
EST: gi|71331352|gb|DR802510.1|DR802510
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
EST: gi|67011685|gb|CO440434.1|CO440434
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
EST: gi|149103442|gb|EE288835.2|EE288835
EST:     ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAG                         GTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG
genomic: ATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATG

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), 48 (downstream exon)
Score: 125

TGAATCTGAGATTACCCAAGACGCCACTCTGAAGCTGCTACATTCACTGGATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

TGAATCTGAGATTACCCAAGACGCCACTCTGAAGCTGCTACATTCACTGGATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 214

TGAATCTGAGATTACCCAAGACGCCACTCTGAAGCTGCTACATTCACTGGATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 120

TGAATCTGAGATTACCCAAGACGCCACTCTGAAGCTGCTACATTCACTGGATCCAATTAAAAATAAGGACACCAAGGATAGGGGCACATTACATCTTAAGgttagtgtgg ... aacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagtaaattccggatcaatttgatggtgctaatatattattttcaacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA
                           tgctaat  putative branch site (score: 120)
                                               cccttc  putative PPT
                              taatatattattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgtggactgccagcttgacaaatgttatttggctggaaaaattaagagtaaattccggatcaatttgatggtgctaatatattattttcaacccttcagGTAAAGTACCACCCCTTTACAAAGGAAGAGCAGCTGGAAGCCCTAGAGATGGAAAAACAAGCCATAGAGGAGAGGAAGCGTCTGAAGGAGGCTGGGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG