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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttcacatatcactggattgctaccattcccttcctagcatatatgacacttattatctatgtgtatgtaaccatgtattttggatttttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA

Basic information

species Zea mays
transcript GRMZM2G410515_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 5
--atgttcacatatcactggattgctaccattcccttcctagcatatatgaca---cttattatctatgtgtatgtaaccatgtattttggatttttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA
   |  |  |||          |  |  | | | |  |    ||||| |||||    | ||| | |   ||||||||||||| ||  ||     ||||||||||||||||||||||||||||||||||||  |||||||||||||| | ||| | ||||| || || ||||| |||||||| |||||||| ||||||||||||||
ttttccttccatgctcacactgttttgtcgtccacaacagtacatatgtgacattgttcattttgtgcctgtatgtaaccatatacctt-----tttggtttaagTTGGAGCTTATCCCAACATACAGAACTTGTTTGGCGAGCTTGGTATTAATGATCGGTTGCAATGGAAGGAACACTCCATGATATTTGCCATGCCAAACAA
















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|211417839|gb|FL018169.1|FL018169
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211005245|gb|FL018195.1|FL018195
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211002469|gb|FL018188.1|FL018188
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCA-CATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211417840|gb|FL018170.1|FL018170
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCAACATACAG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAG
EST: gi|211417848|gb|FL018178.1|FL018178
EST:     TGGAAGGATGAAGATGGAGNAT-GGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TGGAAGGATGAAGATGGAG-ATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211002475|gb|FL018194.1|FL018194
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCC-AACATACAGAAATCTGTT-GGCGAGCTTAGGATTGAG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAA-TCTGTTTGGCGAGCTTAGGATTGAG
EST: gi|71765383|gb|DR963320.1|DR963320
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211005249|gb|FL018199.1|FL018199
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCC-AACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211417847|gb|FL018177.1|FL018177
EST:     TTGGAAGGATGATGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCA-CATACAGAATCTGTTTGGCGAGCTTANGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211002464|gb|FL018183.1|FL018183
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCGGTT                         TTGGAGCTTATCCCA-CATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|76294009|gb|DV033577.1|DV033577
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|78075888|gb|DV504322.1|DV504322
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211417850|gb|FL018180.1|FL018180
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGAGCTTATCC-AACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGG
EST: gi|211415305|gb|FL018166.1|FL018166
EST:     TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTT                         TTGGGAGCT-ATCCCCACATACAGAATCTGTTTGGCGAGCTTAGGGAT-GA
genomic: TTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGG-AGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGG-ATTGA

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: 48 (upstream exon), 45 (downstream exon)
Score: 64

GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 136

GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 82

GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 110

GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTgtaagttaca ... ttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgacacttattatctatgtgtatgtaaccatgtattttggatttttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA
                      atgtaac  putative branch site (score: 110)
                                          ttttt  putative PPT
                                 tattttggattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttcacatatcactggattgctaccattcccttcctagcatatatgacacttattatctatgtgtatgtaaccatgtattttggatttttggtttaagTTGGAGCTTATCCCAACATACAGAATCTGTTTGGCGAGCTTAGGATTGAGGATCGTTTACAGTGGAAAGAACACTCTATGATATTCGCCATGCCAAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - cactgga
- - - - - - - - - - tgctacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catgtat