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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatccagcctaggccctggtgtgatagtactgtgcggtatccattagcatgaaaaaaatcaatctattttctggagttacagcatggtttattga...

Basic information

species Zea mays
transcript GRMZM2G151977_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os12g03190.1 (Oryza sativa), 5'ss of exon 10
GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatccagc-------ctaggccc---------------tggtgtgatagtactgtgcggtatccattagcatgaaaaaaatcaatctattttctggagttacagcatggtttattga---------------------------------------
|||||||||| || ||||| || ||||| ||||||||| | |  |||||||||| || |||||| ||||||||||| |||||| ||||||||||| ||||||||| ||||          ||| ||||               | ||||  |  ||||    |    | |||  || || | |  |    ||||| | || | ||     | |   | || |                                       
GTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAAGAGTAAAGGCAGCATCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtacgtatccttttattgtgctatgcccatctgaatcactaagtagtgttttgatactcaaagcatactattgtca-gagacacgtaggcctattctgtgcattttgtaaaggtacttttaatggtagtgtagactgtagagtaacatccccattttgtag

upper sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g03470.1 (Oryza sativa), 5'ss of exon 10
GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatccagc--ctaggccctggtgtgatagt-actgtgcggtatcc----attagcat----------gaaaaaaatcaatctattttctggagttacagcatggtttattga---------------------------------
|||||||||| || ||||| || ||||| ||||||||| | |  |||||||||| || |||||| ||||||||||| |||||| ||||||||||| ||||||| | ||||      |  ||  ||   |   | | |||     || |      | ||||||          || | |  |    | ||||    |  ||     | ||||  || |                                 
GTGGTTTAGTACAGCTTGATAAAAGCATTGAAGAAAGAGTAAAGGCAGCATCTTTGAAAGGAAATGTTCTTCGCTATGTCTGTAAGATTGAAAGCACAGGgtatgtatccttttattgtgctatgccctctgaatcactaattagtgtttcaatactagcatactattgtcagagacacgtaggcccatttctgtgcattttgtaaaggttctttcaatggtagtgtagagtaacatccccattttgtag
















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|86473774|gb|DY240144.1|DY240144
EST:     TCTTCGAGAGGAAACGTTTTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTTTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|67018901|gb|CO447650.1|CO447650
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAAGTATGCCTTAAAGAGTTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|37373740|gb|CF623185.1|CF623185
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|101393898|gb|EB818882.1|EB818882
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTTTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|37391307|gb|CF632895.1|CF632895
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|67013499|gb|CO442248.1|CO442248
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAAGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|32803400|gb|CD955636.1|CD955636
EST:     TCTTCGAGAGGAAACGTTCTTCGCTATGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAAGTAGGCCTTA
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTA
EST: gi|94478774|gb|EB707732.1|EB707732
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|5761968|gb|AI967016.1|AI967016
EST:     ACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAAAGCTCCCAAAGGATTTTGCGCTGGGTAGATT
genomic: ACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|37386125|gb|CF630238.1|CF630238
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|18181178|gb|BM382388.1|BM382388
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|93016571|gb|EB642091.1|EB642091
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTTTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|60349556|gb|DN216529.1|DN216529
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
EST: gi|40334075|gb|CK368145.1|CK368145
EST:     TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGG                         GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT
genomic: TCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATT

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), 43 (downstream exon)
Score: 41

GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 42

GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG


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

GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 67

GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatcc ... tggtctgcagGTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTTTAGTGCAACTTGACAAGAGCATGGAAGAAAGAATCAGAGCAGCATCTTCGAGAGGAAACGTTCTTCGCTACGTCTGTGAGATTGAAAGCGCAGGgtacgcatccagcctaggccctggtgtgatagtactgtgcggtatccattagcatgaaaaaaatcaatctattttctggagttacagcatggtttattga

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaat