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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaggggaaaaaatccttcgccttcgcctccgcttcccccttctctccatctccccttccccttctcgcgcctgaccaatcctctgttcctgctcttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG

Basic information

species Zea mays
transcript GRMZM2G156019_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G156019_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g72330.1 (Oryza sativa), 3'ss of exon 2
gtaaggaggggaaaaaatcct-tcgccttcgcctccgcttcccccttctctccatctc-cccttccccttctcgcgcct-----gaccaatcctctg--ttcctg--ctcttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG
      || | |  | ||| | |    ||    || | |||    |||| |  |  |  |   | |  | || ||          |  || | | ||  || |||  || ||| |||||||||| || || || || || |||||||||||||||||||| ||||||||||| || |||||||||||||| ||||||
---gtcagtgaatgagatcttgttctttttttttctgtttcatgtttcttttgaattggcttctgctgtgcttgcaatccaggaaattaaccatgtggttttctgaactgttggtacagGAGATTGATGTCAACCTGATAATCACTGACTACTGCATGCCTGGCATGACAGGGTATGATCTGCTCAAGAGGGTGAAG
















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|91048093|gb|EB158511.1|EB158511
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|91049479|gb|EB159897.1|EB159897
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|211439400|gb|FL402881.1|FL402881
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|148975637|gb|EE025768.2|EE025768
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCANGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|89759374|gb|DY688232.1|DY688232
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|148971158|gb|EE022012.2|EE022012
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|149112392|gb|EE295266.2|EE295266
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGA
EST: gi|76281690|gb|DV021258.1|DV021258
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|149096713|gb|EE182486.2|EE182486
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|211215269|gb|FL414788.1|FL414788
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|211097795|gb|FL409141.1|FL409141
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
EST: gi|211324213|gb|FL425817.1|FL425817
EST:     TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAG                         GAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA
genomic: TGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACA

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: 62

TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 72

TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 65

TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 62

TGACCACGGTGGATTCCGGGAGCAAGGCGCTGGAGCTGCTGGGGCTGAGGGACGCGTCGTCGCCGTCTCCGTCCTCGCCTGACCACCAGgtaaggaggg ... cttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccccttccccttctcgcgcctgaccaatcctctgttcctgctcttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG
                    gcctgac  putative branch site (score: 62)
                              tcctctgttcctgctc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaggggaaaaaatccttcgccttcgcctccgcttcccccttctctccatctccccttccccttctcgcgcctgaccaatcctctgttcctgctcttgctacagGAGATCGACGTGAATCTCATCATCACTGACTACTGCATGCCAGGCATGACAGGATACGATCTGCTCAAGAGAGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA