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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctgctcctccatctactctctctctcatcgttgtttgcactgcatagtgcatggtatgctaggtagcatcagctacgaattctaaagtactgcaacaagagaatacttgctaaccaaacgcatggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA

Basic information

species Zea mays
transcript GRMZM2G118003_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G118003_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g49600.1 (Oryza sativa), 3'ss of exon 9
gtacgctgctcctccatctactctctctctcatcgttgtttgcactgcatagtgcatggtatgctaggtagcatcagctacgaattctaaagtactgcaaca-agagaatacttgctaaccaaacgcatggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA
||| || | |  ||  |    ||  ||||        | ||   ||    | |||||  ||    | ||  |   |   |  |||||  |||||    |||  | | ||   ||| | | | | || ||    ||  |||| |||||||| ||||| |||||||  ||   |||||||||||| || ||||||||| ||||| ||||||| |||||||| ||  ||  |||||| || |
gtatgcag-taatcagttgtatccttctccagcttcagattcttcta-gcactgcattctac-tgacgtgaccaaactgataaattcagaagtaacataactcataaaacctttgttgatccatcg-atctttac--agGCAAATTCTAATTGGCTTTACATCGTGCCATGGGGGATGTACGGATGTGTGAACTACATCAAGCAGAAGTACGGGAATCCGACAGTCGTCATAACTGAAA
















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|31664105|gb|CD573285.1|CD573285
EST:     TTGCACGCAATGGCAAGCCGATTGGGCCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|31909830|gb|CD651115.1|CD651115
EST:     GGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: GGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|101393332|gb|EB818597.1|EB818597
EST:     CAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: CAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|67010696|gb|CO439445.1|CO439445
EST:     CGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: CGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|5069778|gb|AI737743.1|AI737743
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTGTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|4388066|gb|AI491238.1|AI491238
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|28982563|gb|BQ538179.2|BQ538179
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|29543409|gb|CB603805.1|CB603805
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|37384568|gb|CF629372.1|CF629372
EST:     TGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|19822253|gb|BQ048277.1|BQ048277
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|4776298|gb|AI665301.1|AI665301
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTNTAAGTGGCTTTACATCGCNCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|24767182|gb|CA402326.1|CA402326
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|44900753|gb|CK827298.1|CK827298
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|148934073|gb|EC878087.2|EC878087
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|60352240|gb|DN219213.1|DN219213
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|60339007|gb|DN205980.1|DN205980
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|60350347|gb|DN217320.1|DN217320
EST:     TTCAATATGTTTTTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TT------G------CACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|31359746|gb|CD444103.1|CD444103
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|26457057|gb|CA828640.1|CA828640
EST:     TGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGCATGTACGGGTGCGT
genomic: TGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGG-ATGTACGGGTGCGT
EST: gi|19822445|gb|BQ048469.1|BQ048469
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|40334112|gb|CK368182.1|CK368182
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|211275276|gb|FL057455.1|FL057455
EST:     AGTTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGAC-GGAATGTACGGGTGCGTG
genomic: AGTTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|60353267|gb|DN220240.1|DN220240
EST:     TTGC-CGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|148928823|gb|EC873677.2|EC873677
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|60336744|gb|DN203717.1|DN203717
EST:     GCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: GCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|32165128|gb|CD670446.1|CD670446
EST:     CGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: CGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
EST: gi|60338477|gb|DN205450.1|DN205450
EST:     TTGCACGCAATGGCAAACCGATTGGACCACAG                         GCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG
genomic: TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTG

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), 49 (downstream exon)
Score: 1213

TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 969

TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1024

TTGCACGCAATGGCAAACCGATTGGACCACAGgtacgctgct ... ggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctaaagtactgcaacaagagaatacttgctaaccaaacgcatggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA
                             tgctaac  putative branch site (score: 1024)
                       aatactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctgctcctccatctactctctctctcatcgttgtttgcactgcatagtgcatggtatgctaggtagcatcagctacgaattctaaagtactgcaacaagagaatacttgctaaccaaacgcatggacacgtagGCGAATTCTAAGTGGCTCTACATCGCCCCGACGGGGATGTACGGGTGCGTGAACTACCTCAAGGAGAAGTATGGGAATCCAACGATCTACATAACGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT