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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagagattttgatttttaaacccacccaatcccctccaacccacatggattgagatgaaaatgaacaagctctaattgtgtttctccttttgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT

Basic information

species Zea mays
transcript GRMZM2G017329_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017329_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g15110.1 (Oryza sativa), 3'ss of exon 5
--------------tagagattttgatt----tttaaacccacccaatcccctccaacccacatggattgagatgaa-aatgaacaagctctaattgtgtttctccttttgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT
              | | |||  |   |    ||     | |    || |  |  | | |        | | ||      |     |  ||| ||||||| ||||||  | |    |||||||||||||  ||||||| ||||| || ||| |||||||| | || || |||||||| || || |||||||||||||||||||||||||||||||| ||
gtatgtggtaccgttggggatgatagatgggattatgtgctatttgatacgttgaagcacgaggctgctcatatatctggtatgttatatctgattgtgtatctcctcctatactgcagATGACATTGACACCCATATCGAGAATGCTGTTATAGCGACTACACAAGCAAAAGGCCAACTCTCTAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCGCT
















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|37380366|gb|CF626991.1|CF626991
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|18176906|gb|BM378116.1|BM378116
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|78119338|gb|DV537722.1|DV537722
EST:     AATCTTCAAAGATCTCGCTGTGGTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|84980293|gb|DW530642.1|DW530642
EST:     GATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|78075157|gb|DV503591.1|DV503591
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|37380903|gb|CF627296.1|CF627296
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|6448408|gb|AW181174.1|AW181174
EST:     TGTGCTAGTCCATGACCAAGGAGCAATGATAG                         ATGCCATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: TGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|32868289|gb|CF007971.1|CF007971
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGACCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|15199008|gb|BI423606.1|BI423606
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGACCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|71760533|gb|DR958470.1|DR958470
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|67026173|gb|CO454922.1|CO454922
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|78083868|gb|DV512261.1|DV512261
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|71758925|gb|DR956862.1|DR956862
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|116820906|gb|EC864174.1|EC864174
EST:     GAGC-ATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: GAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|16925613|gb|BM078681.1|BM078681
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|32941316|gb|CF046135.1|CF046135
EST:     AATCTTCAAAGATCTCGCTGTGCTAGTCCATGACCAAGGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: AATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
EST: gi|211265555|gb|FL463513.1|FL463513
EST:     GGAGCAATGATAG                         ATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA
genomic: GGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTA

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), 48 (downstream exon)
Score: 147

AGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 323

AGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 284

AGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 275

AGGGATCAGGGAATACAAGAGATTCAGCACCAAATCACTGAAGTAAATGAAATCTTCAAAGATCTCGCTGTGCTAGTCCATGATCAAGGAGCAATGATAGgtgtgtggcc ... tgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattgagatgaaaatgaacaagctctaattgtgtttctccttttgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT
                        ctctaat  putative branch site (score: 275)
                              ttgtgtttctcctttt  CT-rich tract
         atgaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagagattttgatttttaaacccacccaatcccctccaacccacatggattgagatgaaaatgaacaagctctaattgtgtttctccttttgtgaaccagATGACATTGATTCCCATATAGAGAACGCCGTTGTAGCGACTTCGCAGGCTAAAGGCCAGCTTTCAAAGGCTGCTAAAACTCAGAAGTCGAACTCTTCTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - -ccaccca
- - - - - - - - - - - - - - - -ccctcca
- - - - - - - - - - - - - - - - - - - - -cacatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gatgaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caagctc