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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttttgacttttttttatttctaccagttttctcagtatttgtgtttgatgtacacagtttcactagaatgtttctaatggttgtcttttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGGTTAAGTTTGTAAAG

Basic information

species Zea mays
transcript GRMZM2G124886_T02
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T02 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 24
-ttgttttgacttttttttatttctaccagttttctcagtatttgtgtttgatgtacacagtttcactagaatgtttctaatggttgtcttttcttt-gcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCA-AGTGGTTAAGTTTGTAAAG
  ||    |  || ||      | |     |     ||   |||||| ||| | ||||    ||   | ||   |||||||    ||||||  |||| |||||  |||||||||| |||||||| |||| |||||||||||| |   | | || || || ||||||||
tctgaccagttttcttagacagtttgaacataggagcaaattttgtgcttgctatacattagttg--ttgatgttttctaactactgtcttgccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG

upper sequence: GRMZM2G124886_T02 (Zea mays), 3'ss of exon 24
lower sequence: LOC_Os02g11840.2 (Oryza sativa), 3'ss of exon 15
-ttgttttgacttttttttatttctaccagttttctcagtatttgtgtttgatgtacacagtttcactagaatgtttctaatggttgtcttttcttt-gcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCA-AGTGGTTAAGTTTGTAAAG
  ||    |  || ||      | |     |     ||  ||||||| ||| | ||||    ||   | ||   ||||||| |  | ||||  |||| |||||  |||||||||| |||||||| |||| |||||||||||| |   | | || || || ||||||||
tctgaccagttttcttagacagtttgaacatgagagcaaaatttgtgcttgctatacatgagttg--ttgatgttttctaacgactatcttgccttttgcagTATTGACTCCTGACCAATAGTGAATCAGCGGGACAGCAACCTGATACACTGATTCAGCTTGTAAAG
















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|5847331|gb|AW000410.1|AW000410
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAAC
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAAC
EST: gi|5871516|gb|AW017987.1|AW017987
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
EST: gi|101392738|gb|EB818300.1|EB818300
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
EST: gi|37374749|gb|CF623760.1|CF623760
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
EST: gi|6031398|gb|AW076300.1|AW076300
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
EST: gi|78021428|gb|DV489815.1|DV489815
EST:     AATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
EST: gi|211483407|gb|FL444449.1|FL444449
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
EST: gi|211053668|gb|FL029981.1|FL029981
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTSGATCAACGGGACAGCAACTTT
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTT
EST: gi|120480718|gb|EH210975.1|EH210975
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAKCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
EST: gi|67031167|gb|CO459916.1|CO459916
EST:     AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGG                         TGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG
genomic: AACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGG

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), 49 (downstream exon)
Score: 199

GGAGTAGAAGAAAGTCAGGATGAAGCTGTTGAGGTTGAGGCTGAGGATTCAACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGGTTAAGTTTGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

GGAGTAGAAGAAAGTCAGGATGAAGCTGTTGAGGTTGAGGCTGAGGATTCAACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGGTTAAGTTTGTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 364

GGAGTAGAAGAAAGTCAGGATGAAGCTGTTGAGGTTGAGGCTGAGGATTCAACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGGTTAAGTTTGTAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 307

GGAGTAGAAGAAAGTCAGGATGAAGCTGTTGAGGTTGAGGCTGAGGATTCAACTGATGGTGCTGTCCTTGTGAATGGAAACAATAGTGAGGAACAGTGGGgtatgaaaaa ... ttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGGTTAAGTTTGTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgatgtacacagtttcactagaatgtttctaatggttgtcttttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGGTTAAGTTTGTAAAG
                             ttctaat  putative branch site (score: 307)
                                      ttgtcttttctttgc  putative PPT
                            tttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttttgacttttttttatttctaccagttttctcagtatttgtgtttgatgtacacagtttcactagaatgtttctaatggttgtcttttctttgcagTGCTGACTCCTGAGCAATAGTGGATCAACGGGACAGCAACTTTGCAAGTGGTTAAGTTTGTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
-tgttttg
- - - - - - - - - - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - -gatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggttg