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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgttggttctcccttttggtttggtattctattgtgcacttaggtttgtttttgttatttgtactgatattctattagtttcctctctgctgtgcagtattgaatatgtctttgtttggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA

Basic information

species Zea mays
transcript GRMZM2G015132_T01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os07g22720.2 (Oryza sativa), 3'ss of exon 13
gtaattgttggttctcccttt-----tggtttggtat-tctattgtgcactta-----ggtttgtttttg-------ttatttgtactgatattctattagtttcctctctgctgtgcagtattgaatatgtctttgtttggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA
||||||    |||   | | |     ||||||  ||| ||||    |  |  |     || |||||   |        ||||| |  |  |   || |   ||| || ||||   | || |  ||||| | ||||  |||| | | |||||||||||| |||| ||||||||||||||||||||||| ||||| ||||||||||||||||| || ||
gtaattaccagtttctcgtgttaccgtggtttcttatgtctaccaagtgccaaccactggattgttgcagattcagcctatttatgttcgtggactgtccattttct-tctgacctccaattctgaatttatcttaatttgatgtacagGCTGCAGCTCTGGCTCTTCGAAAGGTCCCTCAGTGTAATAGCTCCTGGATGAATGATTTTATCCGCCA

upper sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g01500.1 (Oryza sativa), 3'ss of exon 13
gtaattgttggttctcccttttggtttggtatt--ctattgtgcactta-ggtttgtttttgttatttgtactgat----attctattagtttcctctctgctgtgcagtattgaatatgtctttgtttggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA
|||||||  | ||     |||    |   ||    | |||| |   |    | |||  | | | || | ||    |    |  || ||| ||| ||| |||   | |||   |||||   ||||  |||| | |||||||||||||| |||| ||||||||||||||||||||||| ||||| ||||||| ||||||||| || ||
gtaattgccgttttcttgtttcttatgtctaccaaccattgagttgtcgcagattgggtgtatgatgtatatcagttcacagactgttaattttctc-ctgacctccagatctgaattgatcttaatttgatgtgcagGCTGCAGCTCTGGCTCTTCGAAAGGTCCCTCAGTGTAATAGCTCGTGGATGAGTGATTTTATCCGCCA
















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|74235054|gb|DT642968.1|DT642968
EST:     AGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAG                         GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
genomic: AGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
EST: gi|71333154|gb|DR803611.1|DR803611
EST:     GAAAATATCAATTAATGATCTTGTCATCAAG                         GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
genomic: GAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
EST: gi|32840355|gb|CD980036.1|CD980036
EST:     AGGATGCTTCTGGTGGAAAGAAAATATCGATTAATGATCTTGTCATCAAG                         GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
genomic: AGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
EST: gi|32938642|gb|CF043461.1|CF043461
EST:     AGGATGCTTCTGGTG-AAAGAAAATATCGATTAATGATCTTGTCATCAAG                         GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
genomic: AGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
EST: gi|32932311|gb|CF037123.1|CF037123
EST:     AGGATGCTTCTGGTGGAAAGAAAATATCGATTAATGATCTTGTCATCAAG                         GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
genomic: AGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
EST: gi|211011840|gb|FL066266.1|FL066266
EST:     CAATTAATGATCTTGTCATCAAG                         GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
genomic: CAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
EST: gi|78091151|gb|DV519525.1|DV519525
EST:     CAATTAATGATCTTGTCATCAAG                         GCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG
genomic: CAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATG

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: 48 (upstream exon), 47 (downstream exon)
Score: 133

GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 286

GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 187

GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 306

GTTGCGAGGTGAACTGAACCCACTGCAGGATGCTTCTGGTGGAAAGAAAATATCAATTAATGATCTTGTCATCAAGgtaattgttg ... tggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattagtttcctctctgctgtgcagtattgaatatgtctttgtttggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA
                                     tctttgttt  CT-rich tract
                          tattgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgttggttctcccttttggtttggtattctattgtgcacttaggtttgtttttgttatttgtactgatattctattagtttcctctctgctgtgcagtattgaatatgtctttgtttggtatgcagGCTGCAGCTTTGGCCCTTCGAAAGGTCCCTCAGTGTAACAGCTCATGGATGAATGATTTTATTCGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA