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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcccttccctaacaccccctgtgcacactgatgacaggcagacagagaaatcacactgccccctgatgattttatttccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC

Basic information

species Zea mays
transcript GRMZM2G113267_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113267_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g01830.1 (Oryza sativa), 3'ss of exon 6
gtaagtcccttccctaacaccccctgtgcacactgatgacaggcagacagagaaatcacactgcccc-ctgatgattttatttcct-------tgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC
|||  |||  |||  |  |  ||    ||| ||      ||  || | ||||    ||   |  |   | ||||  ||| |||  |       || |||||||||||||| ||||| ||||||||||||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||  |||||||    |
gtagttcctctcc--agtattcca---gcatacgatctgcaaccaaaaagagtttgcagtgtatctgacagatggattttttttttgtggtggtgttagATTGAGACATGCAGAAAGGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCTTCGCAGATCAAAGTGCTCCCCTTCCATGCTGCATTGGATCAACAAC
















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|71308808|gb|DR790647.1|DR790647
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|71444583|gb|DR825633.1|DR825633
EST:     AGATTATCGAGGAGTCTCCTGGCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|149111889|gb|EE191046.2|EE191046
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|149086256|gb|EE175797.2|EE175797
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|149082649|gb|EE171854.2|EE171854
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTTTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|78026219|gb|DV494606.1|DV494606
EST:     CGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: CGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|31357346|gb|CD441703.1|CD441703
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|149083804|gb|EE173175.2|EE173175
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTTTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|149027555|gb|EE046565.2|EE046565
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|32840583|gb|CD980264.1|CD980264
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGACACATGTAGAAAAGTAGAGAATGCGCTGAGGCGGGTTGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|71317553|gb|DR795508.1|DR795508
EST:     GATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGC-ACAAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAA
genomic: GATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAAC-AAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAA
EST: gi|4753537|gb|AI657447.1|AI657447
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAACCAATTGTTTTTTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGNTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|76285737|gb|DV025305.1|DV025305
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTG-TTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|71444660|gb|DR825710.1|DR825710
EST:     AGATTATGGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGTTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
EST: gi|71444661|gb|DR825711.1|DR825711
EST:     AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAG                         ATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG
genomic: AGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAG

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: 45 (upstream exon), 48 (downstream exon)
Score: 85

AGAAAAGAATCCAGAAACCGCCTTTTCGAACAAGAAAACAGCGCTTTTGAAGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 140

AGAAAAGAATCCAGAAACCGCCTTTTCGAACAAGAAAACAGCGCTTTTGAAGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 39

AGAAAAGAATCCAGAAACCGCCTTTTCGAACAAGAAAACAGCGCTTTTGAAGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 116

AGAAAAGAATCCAGAAACCGCCTTTTCGAACAAGAAAACAGCGCTTTTGAAGATTATCGAGGAGTCTCCTGTCCGCAAAACAATTGTTTTCTGCAACAAGgtaagtccct ... tccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacaggcagacagagaaatcacactgccccctgatgattttatttccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC
                             ccctgat  putative branch site (score: 116)
                                      ttttatttccttgct  putative PPT
                                tgatgattttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcccttccctaacaccccctgtgcacactgatgacaggcagacagagaaatcacactgccccctgatgattttatttccttgctagATTGAGACATGTAGAAAAGTTGAGAATGCGCTGAGGCGGGTGGACAGGAAGGCCTCGCAGATCAAAGTTCTCCCCTTCCATGCTGCGCTGGATCAGGCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA