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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcatgacttgtatggccctaggttgtcaacgcagtgtttcgattgtgccattgttgctattacttgttgatagcttaaacatcattgatttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT

Basic information

species Zea mays
transcript GRMZM2G128114_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G128114_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g07760.2 (Oryza sativa), 3'ss of exon 1
attcatgacttgtatggccctaggttgtcaacgcagtgtttcgattgt--gccattgttgctattacttgttgatagcttaaacatcattgatttcc---cgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT
    |    |||  |      | |   |  |  ||||||||  ||     |    ||    | ||| ||||||||   | ||||| ||||  |||||   | ||||| ||||||||||||||||| |||   ||||| || ||||||| ||||||||||| ||||||||||||||| || ||||| |||||||||||||||||||
----acacgttgc-tattggaaagaactttatccagtgtttatatctctagtttatgacagtgttagttgttgatgattaaaacaccattcttttcctctcttagGTTCAAAATCCAGCAACTGGAGAGACTCTTGCCAATGTGTCCTGTATGGGCAGCAAAGAAACATCTGATGCAATAGCTTCAGCTCACAGTACATTCTATT
















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|211450282|gb|FK953943.1|FK953943
EST:     GGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAG                         GTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGC
genomic: GGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAGgtacccgtca ... tttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGC
EST: gi|211509962|gb|FL438235.1|FL438235
EST:     GGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAG                         GTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGC
genomic: GGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAGgtacccgtca ... tttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGC
EST: gi|67040351|gb|CO466606.1|CO466606
EST:     GGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAG                         GTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGC
genomic: GGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAGgtacccgtca ... tttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGC

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), 47 (downstream exon)
Score: 23

GAGCGCCGCGATGGAGAAGATCCGCGCCGCGGGTCTGCTCAAGACGCAGGGGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAGgtacccgtca ... tttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 59

GAGCGCCGCGATGGAGAAGATCCGCGCCGCGGGTCTGCTCAAGACGCAGGGGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAGgtacccgtca ... tttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 32

GAGCGCCGCGATGGAGAAGATCCGCGCCGCGGGTCTGCTCAAGACGCAGGGGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAGgtacccgtca ... tttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT


Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 62

GAGCGCCGCGATGGAGAAGATCCGCGCCGCGGGTCTGCTCAAGACGCAGGGGCTCATCGCCGGACAGTGGGTCGACGCATACGATGGCAAGACCATCGAGgtacccgtca ... tttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgccattgttgctattacttgttgatagcttaaacatcattgatttcccgtagGTGCAAAATCCAGCAACTGGTGAGGTCCTTGCAAACGTGTCCTTTATGGGCAGCAGAGAAACATCTGATGCTATTGCTTCTGCTCACAGTACATTCTATT
                                       cattgat  putative branch site (score: 62)
                                             tttcccgt  CT-rich tract
              tattactt  TA-rich tract