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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctgaggttcagagcttcagatatctgagagtagctgtgttagctcgtctgtttgtaggaacagtgccttagttaccttgcatggttgcacatttttgtggatctgatcatccctctttgttcatggttctatcgttag

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g42520.3 (Oryza sativa), 5'ss of exon 4
TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctgagg-ttcaga--gcttcag-------------------atatctgagagtagct-gtgttagctcgtctgtttgtaggaac--agtgcctta-gttaccttgcatggttgcacatttt---tgtggatctgatcatccc--tctttgttcatggttcta--tcgttag
|||||||||||||||||||| || ||||| || ||||||||||| ||||  |||||||| ||||||||| | |||||||||||||| ||||| ||| ||||| |||  | |||  |||||  || ||||                   |   ||    ||||||  |  | | |   ||| |  || |||    |||   || |||    ||||    ||| ||||||    |||  ||||||||| |   |||| ||||||   | ||  ||  |||
TTCAGCGAGTACACGGTTGTGCACTCCGGTTGCGCGGTGAAGGTCGGCCCAACCGTGCCGATGGACAGGATATGCCTGCTGAGCTGTGGTGTATCTGCAGgtgaattttaagggctcagatggcatcagtgtttttactttatcttccacgcctttctgtagcttatacttggtttactgatgctaagaattaggtgtgctatgttgttctgcacttctgcgcattttaaccgtgtctctgatcattcatgtcttcgttcatttctgtatttcactag
















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|71771533|gb|DR969470.1|DR969470
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         ---TC--TG--G-----AATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|14203856|gb|BG837533.1|BG837533
EST:     GACCGTSCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTGCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|149083974|gb|EE173360.2|EE173360
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|5296121|gb|AI782996.1|AI782996
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTGCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|50322631|gb|CO517757.1|CO517757
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCA
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCA
EST: gi|6194720|gb|AW146824.1|AW146824
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTGCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|5895803|gb|AW037049.1|AW037049
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTGCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|5895869|gb|AW037115.1|AW037115
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTGCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|29946549|gb|CB816205.1|CB816205
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|148957215|gb|EC903225.2|EC903225
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|101382109|gb|EB813110.1|EB813110
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
EST: gi|6020665|gb|AW065698.1|AW065698
EST:     GACCGTGCCAATGGACAGGGTGTTTCTGCTGAGCTGCGGTGTGTCTGCAG                         GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG
genomic: GACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAG

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), 46 (downstream exon)
Score: 140

TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 203

TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 345

TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 287

TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctg ... ctatcgttagGACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGCGAGTACACGGTTGTCCATTCCGGATGTGCGGTGAAGGTTGGCCTGACCGTGCCAATGGACAGGGTGTGCCTGCTGAGCTGCGGTGTGTCTTCAGgtaaatcctgaggttcagagcttcagatatctgagagtagctgtgttagctcgtctgtttgtaggaacagtgccttagttaccttgcatggttgcacatttttgtggatctgatcatccctctttgttcatggttctatcgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC