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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatatttttttacttgatccaaaataaatgtaggtcatttctattgttatgcatgttagaatctacgccggagagacaaccctgcaggttgccggcgag...

Basic information

species Zea mays
transcript GRMZM2G413652_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G413652_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g49050.1 (Oryza sativa), 5'ss of exon 4
CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGctatcgaacttgtacaaagctgatttgctactctgtgaatctggaggaggtatatttttttacttgatccaaaat-aaatgtaggtc---atttctattgttatgcatg---ttagaatctacgccgg---------agagacaaccctgcaggttgccggcgag------------------------------------------------------------------
|| || || || || || ||||||||||||||||| ||||||||||| || ||||| ||||||| |||||||||||| || ||||||||||||||||||||||| |   | |       |||| ||   | | |  ||   |||  | || | ||| |||   ||  || | |  | ||         | |||||   ||| |  ||  | |                                                                      
CACGCTGCAATACGTGAGGACATCAGCATAAATCTAGGTCCTCTGGAAGAACTATCAAACTTGTGCAAAGCTGATTTACTCCTCTGTGAATCTGGAGGAGgtatttaactctctgaatcccaacattggaagcacttctctattctttttatcatgtatgcttttgcaaaccatcctggcatcctgctacagacagaactgta--ttatctgtttattttggaaggcattgttatgctaaatccaaaatgaagtgctaaaagaaatactgacacttgtgcag

upper sequence: GRMZM2G413652_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G08970.1 (Glycine max), 5'ss of exon 3
CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGctatcgaacttgtacaaagctgatttgctactctgtgaatctggaggaggtatatttttttacttgatccaa--aataaatgtaggtcat---ttctattgttatgcatgttagaatctacgccggagagacaaccctgcaggttgccggcgag
||||| |||||||| || |||||||| || |||||||| || ||||||||||| || ||| | | |||||| ||| | || || ||||||||||| |||||||| |||||||  || ||| ||  | |   ||    |  |   ||| |     |    || || |||| |    | | | | || |  | ||    ||  |   
CATGCTGCTATTCGGGAGGACATCAGTATTAATCTTGGACCGCTGGAGGAGCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttttt-ttttatctaattagttgctgagtattgtagattccacgtcgactagtgatataatcaaaatagtatatataaacgag-agacaaccctc---

upper sequence: GRMZM2G413652_T01 (Zea mays), 5'ss of exon 4
lower sequence: AT2G34470.2 (Arabidopsis thaliana), 5'ss of exon 4
CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGctatcgaacttgtacaaagctgatttgctactctgtgaatctggaggaggtatatttt----tttacttgatccaaaata---aatgtaggtcatttctattgttatgcatgtta--gaatctacgccggagagacaaccctgcaggttgccggcgag-
|| || ||||| || ||||| ||||| || ||| | |||||||| |||||| |||| ||||| | ||| ||||||||||| || |||||||| || ||||||    |||    | ||  |  | |   |||   ||| |     || | ||   || ||  | | |  ||| | | |    |   | |  | |   | |    |  |   
CACGCTGCTATCCGTGAAGATATCAGTATCAATTTGGGTCCTCTTGAGGAGTTATCTAACTTATTCAAGGCTGATTTGCTTCTTTGTGAATCCGGTGGAGgtgaggtttcatttctagctagttcttgatagttaatctgcacgatatatagatttctgtttctcaaggaaccaatgagatatgaataggcttagtgttgtgtgttgcag

upper sequence: GRMZM2G413652_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv10s0003g03120.t01 (Vitis vinifera), 5'ss of exon 8
CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGctatcgaacttgtacaaagctgatttgctactctgtgaatctggaggaggtatattttt----------ttacttgatccaaaataaatgtaggtcatttctattgttatgcatgttagaatctacgccggagagacaaccctgcaggttgccggcgag
||||| || ||||| |||||||||||||| |||||||| ||||| |||||||| || ||||||| ||||| |||  | || |||||||||||||| |||||||  || ||          || | | |      ||   | ||  | ||||||  ||||| |   ||||  ||   |  |  |  |  |||    | |||          
CATGCTGCAATTCGTGAAGACATCAGCATCAATCTTGGCCCTCTTGAGGAGCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgttagtggacacatttcctcacttttcatttttataaatgatttctcatgttaagtg-gttatcattggcatcaaactggtaaca--actggtaat-------

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|78179335|gb|DV549708.1|DV549708
EST:     ACTCTGTGAATCTGGAGGAG                         ATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
genomic: ACTCTGTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
EST: gi|161407584|gb|DW042408.1|DW042408
EST:     ACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG                         ATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
genomic: ACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
EST: gi|211452606|gb|FL416418.1|FL416418
EST:     TATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
genomic: TATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
EST: gi|60358340|gb|DN225313.1|DN225313
EST:     ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
genomic: ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
EST: gi|8577258|gb|BE129895.1|BE129895
EST:     GCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG                         ATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
genomic: GCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
EST: gi|94473481|gb|EB702439.1|EB702439
EST:     AAGACATCAGCATAAATTTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGATGATTTGCTACTCTGTGAATCTGGAGGAG
genomic: AAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
EST: gi|87156249|gb|DY401038.1|DY401038
EST:     GTGAATCTGGAGGAG                         ATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
genomic: GTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
EST: gi|21843537|gb|BQ704118.1|BQ704118
EST:     GTGAATCTGGAGGAG                         ATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
genomic: GTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACA
EST: gi|20300761|gb|BQ163704.1|BQ163704
EST:     ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCAAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
genomic: ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
EST: gi|101386125|gb|EB815103.1|EB815103
EST:     TCCTCGGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGGAG
genomic: TCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGA-GGAG
EST: gi|20300389|gb|BQ163332.1|BQ163332
EST:     ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCAAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
genomic: ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
EST: gi|50326358|gb|CO521484.1|CO521484
EST:     ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG
genomic: ATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAG

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: 47 (upstream exon), 49 (downstream exon)
Score: 84

CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACATTATCGATGTCTCTGGTGGGGACAAGATACCAAGAAAAGGTGGCCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 229

CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACATTATCGATGTCTCTGGTGGGGACAAGATACCAAGAAAAGGTGGCCCTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACATTATCGATGTCTCTGGTGGGGACAAGATACCAAGAAAAGGTGGCCCTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 211

CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatattttt ... ttccatgcagATAACTTGGCAGCTAACTTCAGCAGAGAATTAGCAGACTACATAATCTACATTATCGATGTCTCTGGTGGGGACAAGATACCAAGAAAAGGTGGCCCTGG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGCTATCGAACTTGTACAAAGCTGATTTGCTACTCTGTGAATCTGGAGGAGgtatatttttttacttgatccaaaataaatgtaggtcatttctattgttatgcatgttagaatctacgccggagagacaaccctgcaggttgccggcgag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataaa