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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaacgtgaatgtatctagtctattatttgctcaggttgagattgtatgtttttgcacctttttgtgctaacagcaatttgctattatttatacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC

Basic information

species Zea mays
transcript GRMZM2G163233_T04
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163233_T04 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g36470.1 (Oryza sativa), 3'ss of exon 5
---aaaacgtgaatgtatctagtctatt-atttgctcaggttgagattgtatgtttttgcacctttttgtgctaacagcaat-ttgctattatttatacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC
    | || ||||  | || | | | || ||||  |||  ||     |   ||| |||   |  |||||  || ||| |  | ||  ||  |  ||| || ||||||| | ||||||||  ||||||| |||||  | ||||||||||| ||||| |||||||||||||| ||||| |||||||| || |||||||||||||| |
atctacacttgaac-tgtcaaatatgtttatttattcacatttgagct---tgtctttat-ctcttttgaactgacaaccttctttttacaacctatgcacccagGATTTATTAGATGCGCTGAATCAGCTAGAAATAGGACTCAAAGACAACCTTAAGAAGTTGAGTTCATTTGAGAAGTACAAGCAACAAGTTCTTCTTGGCC
















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|5439388|gb|AI820309.1|AI820309
EST:     GATTGCCGCANATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTT
genomic: GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTT
EST: gi|67023139|gb|CO451888.1|CO451888
EST:     ATTGCCGCANATAGTACAAAACTTGNNAAGCTCA-GCATGGACTGATGAG                         GATCTGTTANATGCTTTGAA
genomic: ATTGCCGCAAATAGTACAAAACTTGA-AAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAA
EST: gi|211415631|gb|FL375675.1|FL375675
EST:     GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|211345775|gb|FL379635.1|FL379635
EST:     GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAGGACCT
genomic: GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAA-AACCT
EST: gi|6760563|gb|AW324662.1|AW324662
EST:     AGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTNTGAATCANCTAGAGGTGGGACTCAAAGANAACCTC
genomic: AGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|60398362|gb|DN231178.1|DN231178
EST:     GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|40334122|gb|CK368192.1|CK368192
EST:     GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|78026061|gb|DV494448.1|DV494448
EST:     GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|71757598|gb|DR955535.1|DR955535
EST:     GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: GATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
EST: gi|37373833|gb|CF623239.1|CF623239
EST:     AAACTTGAAAGCTCAAGCATGGACTGATGAG                         GATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC
genomic: AAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTC

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), 48 (downstream exon)
Score: 120

CTGTAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

CTGTAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 172

CTGTAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 223

CTGTAATTTGCTGGCAAAGGGTGCATTTGCTGCCCAGATGATCGATCTTGGATTGCCGCAAATAGTACAAAACTTGAAAGCTCAAGCATGGACTGATGAGgtgaggaact ... atacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtttttgcacctttttgtgctaacagcaatttgctattatttatacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC
                    tgctaac  putative branch site (score: 223)
                              aatttgctattattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaacgtgaatgtatctagtctattatttgctcaggttgagattgtatgtttttgcacctttttgtgctaacagcaatttgctattatttatacaaccagGATCTGTTAGATGCTTTGAATCAACTAGAGGTGGGACTCAAAGAAAACCTCAAGAAGTTGAGTTCCTTTGATAAGTACAAACAGCAAGTTCTTCTTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG