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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtgctcgatcgttcaattcgcgtgcctttcttttcatttgtgtcattttacatgtaacaatcggatcatccattgttttgtgattattgtgtgttatattaccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA

Basic information

species Zea mays
transcript GRMZM2G118063_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118063_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g08820.2 (Oryza sativa), 3'ss of exon 10
gcaagtgctcgatcgttcaattcgcgtgcctttcttttcatttgtgtcattttacatgtaacaatcggatcatccattgttttgtgattattgtgtgttatattaccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA
          |||    |  ||  |   |  |    |    |    ||||||    | ||| |||    | ||    |||||    ||   ||| || | | |     |||  |||| ||||| || ||||||||||||||||||||||| || ||||||||||||||||| |||||||| |||||||||||||||||||||||  | ||||| |
-------gatgattacactgtttacacacgatgaaatcgggtatcatcatttc---tataa-aattaagtaatgatgtgttt----atatatgtatgatttgtccatgtgtgtagAGTGCAAATTCAAACCAGAGCAACATGCTGATCCTGCAAGAGAGCTGCACGGACGCGTCGGGCTCCTACGTGGTGTACGCGCCGGTGGACATCGTGGCGA

upper sequence: GRMZM2G118063_T02 (Zea mays), 3'ss of exon 10
lower sequence: EFJ19972 (Selaginella moellendorffii), 3'ss of exon 10
gcaagtgctcgatcgttcaattcgcgtgcctttcttttcatttgtgtcattttacatgtaacaatcggatcatccattgttttgtgattattgtgtgttatattaccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA
                                             || |  || | || | |  ||| ||| || ||  | | |   | |   |   |  | |  |  | | ||||     ||||| |  || ||||| ||||| |||||||||||||||||||| ||||  ||||||||   ||| || ||||| ||||||||  |    ||||
---------------------------------------------gtaagctttcttggagctttcg-atcttcgatc-tctagaactgaagcttcttcctgtctctctttccagACTCTCAACTCGACGCACAGCAATATGCTCATCCTCCAGGAGAGCTGCACCGACGACTCGGGCTCGCTCGTAGTTTACGCTCCGGTGGACATCCCAGCCA

upper sequence: GRMZM2G118063_T02 (Zea mays), 3'ss of exon 10
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 10
gcaagtgctcgatcgttcaattcgcgtgcctttcttttcatttgtgtcattttacatgtaacaatcggatcatccattgttttgtgattattgtgtgtta-tattaccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA
                                             || |  || | || | |  ||| ||| || ||   | |   | |      | ||  | |  |  | | ||||     ||||| |  || ||||| ||||| |||||||||||||||||||| ||||  ||||||||   ||| || ||||| ||||||||  |    ||||
---------------------------------------------gtaagctttcttggagctttcg-atcttcgatc--tctagaactgaaacttattcctgtctctctttccagACTCTCAACTCGACGCACAGCAATATGCTCATCCTCCAGGAGAGCTGCACCGACGACTCGGGCTCGCTCGTAGTTTACGCTCCGGTGGACATCCCAGCCA

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|26558595|gb|CA830830.1|CA830830
EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
EST: gi|87156118|gb|DY400907.1|DY400907
EST:     TTGCTAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAGCTCCTACCAGAGCAACTTGCTGATCCTCCGGGAGAGCTGCTCG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
EST: gi|22472184|gb|BU036664.1|BU036664
EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
EST: gi|76017721|gb|DT944891.1|DT944891
EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACG
EST: gi|5566756|gb|AI881622.1|AI881622
EST:     TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAAT                         AGCCCAAACTCCAAC
genomic: TTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAAC

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 3 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 599

TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 78

TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 170

TGGGACATCCTCTCCAACGGTGGCGCAGTCCAAGAAATGGCTCATATTGCAAACGGCCGGGACCATGGCAACTGCGTCTCCCTTCTTCGTGTCAATgcaagtgctc ... ccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatcggatcatccattgttttgtgattattgtgtgttatattaccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA
 atgtaac  putative branch site (score: 170)
                                   tgttatatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaagtgctcgatcgttcaattcgcgtgcctttcttttcatttgtgtcattttacatgtaacaatcggatcatccattgttttgtgattattgtgtgttatattaccatgtacagAGCGCAAACTCCAACCAGAGCAACATGCTGATCCTCCAGGAGAGCTGCACGGACGCATCGGGCTCATACGTGGTGTACGCGCCGGTGGATGTGGTGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG