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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgcttcctagttttttgtagtttcaatttcttgtctgccaaggactggatttggaactgcggtttgtcagtgcgttgtaacattgcttttatggattggaacag

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 19
GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgcttcctagttttttgtagtt-tcaatttcttgtctgccaaggactggatttgg--aactgcggtttgtcagtgcgttgtaacattgcttttatggattggaacag
||||||||||| ||||  || || |||||||| |||||||| |||||||||||||| ||||||||||| ||||||    | |  | | |  |||  || | |   ||||||        | || || |||     |    |  || |    ||  ||  || |                      
GATGGTTCCCTGGATGAGCTTGTTCGCAAGCGCTACCAGAGTTTTGATAGTGAGATCGGTGCCTTGATTGAGgtacaatgtt--caactactttagagctcttgctttcttacacttggatgattgaattgaaacagtaacaattggctcatggtttcaaatag---------------------
















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|60337180|gb|DN204153.1|DN204153
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|29130773|gb|CB381477.1|CB381477
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|76286922|gb|DV026490.1|DV026490
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|3157115|gb|AA979737.1|AA979737
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|60344318|gb|DN211291.1|DN211291
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|32849371|gb|CD989052.1|CD989052
EST:     TACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|211379703|gb|FL400539.1|FL400539
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|32844741|gb|CD984422.1|CD984422
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|32845281|gb|CD984962.1|CD984962
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|211141141|gb|FL467349.1|FL467349
EST:     T-CGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|213179445|gb|FM183428.1|FM183428
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|33097350|gb|CF057310.1|CF057310
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|32856567|gb|CD996248.1|CD996248
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|37385849|gb|CF630089.1|CF630089
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGCGAGATCGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTGGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|60346929|gb|DN213902.1|DN213902
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|33101201|gb|CF061161.1|CF061161
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|211459151|gb|FL411539.1|FL411539
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTG
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTG
EST: gi|32846631|gb|CD986312.1|CD986312
EST:     ACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: ACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|60337495|gb|DN204468.1|DN204468
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|67037452|gb|CO464268.1|CO464268
EST:     TNCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAAGAGACTTTGAG-CGCTAGAGA-GAAAGTCTTTGAGTGGGTT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|32844874|gb|CD984555.1|CD984555
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|6012630|gb|AW062067.1|AW062067
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|60353702|gb|DN220675.1|DN220675
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|110219847|gb|EC901745.1|EC901745
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|74244418|gb|DT652332.1|DT652332
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|110213725|gb|EC895622.1|EC895622
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
EST: gi|60347419|gb|DN214392.1|DN214392
EST:     TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAG                         GCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT
genomic: TCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGT

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: 439

GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 297

GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 137

GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 669

GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgct ... attggaacagGCTGGGAAAGGAGACTTTGAGGCGCTAGAGAAGAAGGTCCTTGAGTGGGGTGAGCCCACTGTTCCGTCCGGCAAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGTTCCCTAGATGCTCTCGTCCGCAAGCGGTACCAGAGCTTTGATAGTGAGATTGGTGCCTTGATCGAGgtatggcgcttcctagttttttgtagtttcaatttcttgtctgccaaggactggatttggaactgcggtttgtcagtgcgttgtaacattgcttttatggattggaacag

- - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - GAGCTT