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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttacccttttatctgtttacacgatggcatatctgtcgttgctaggtatcgcaataactcttgtcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG

Basic information

species Zea mays
transcript GRMZM2G111579_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g27790.1 (Oryza sativa), 3'ss of exon 11
gtttacccttttatctgttta------cacgatggcatatctgtcgttgctaggt-atcgcaataactcttg--tcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
|||| |||||  || ||| ||      ||  ||||||| | || |  ||  || | |  | ||||||| ||   |||| || |||  |||||||||| ||||| ||| | || || |||||||||||||||||||||||||||||||||||||||||||| ||||| |||||||||
gtttgcccttaaatttgtatagctgatcatcatggcatgt-tgacactgtaagcttaatgtaataactatttgttcttttgtatttggcttgcagGTCAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGCATTTTGG

upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os05g03820.3 (Oryza sativa), 3'ss of exon 11
gtttacccttttatctgttta-------cacgatggcatatctgtcgttgc-taggtatcgcaataactcttg--tcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
|||| |||||  || ||| ||       ||  ||||||| | || |  ||  |   ||  | ||||||| ||   |||| || |||  |||||||||||||||| ||| | || || |||||||||||||||||||||||||||||||||||||||||||| ||||| | |||||||
gtttgcccttcaatttgtatagcacgatcatcatggcatgt-tgacactgtatgcttaatgtaataactatttgttcttttgtatttggcttgcagGTTAGGCTGAAGCGATATCTAGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCTTTGCCAGTATTTTGG

upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA05G37850.1 (Glycine max), 3'ss of exon 11
------gtttacccttttatctgtttacacgatggcatatctgtcgttgc-taggtatcgcaataactcttgtcttctg-----------cattctgcttg-cagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
       | ||    |||  |  |||  ||  ||| || | |  | |||| | ||  | |||  |  |    | || ||           |||| | |||  ||||| ||||| ||||||||  | |||||||||||||||||||| || || ||||| ||||||||||| || || |||||||||
gttagtttctattggtttcacaattttaac--tggtatctgttgctttgcattggatttgcagcactttccttgttgtgttattgtaaaccattattcttttcagGTCAGGCTGAAGAGGTATTTGGAGATGAGAGGTGCTGATGGAGGGCCTTGGAGAAGATTGTGTGCTTTACCAGCATTTTGG

upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
lower sequence: GLYMA01G42900.1 (Glycine max), 3'ss of exon 10
gtttacccttttat-ctgtttacacgatggcatatctgtcgttgctaggtatcgcaataactcttgtcttctgcattctgctt---gcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
  ||||   | ||  |||   |    | || || |      |  | |  |  |   |||     |   | | |  ||     |   |||||| ||||||||||||||| | || ||||| |||||||||| |||||| | |   |  || || ||  |||| || ||||||
-gttactaatctacactgaccatgttaagg-attttgaatttctccaaatgccaatatactaagttggtccagtgttaaatcttgtgcagGTCAGGCTAAAGAGGTACATGGAAATGAGGGGTGCTGATGATGGCCCTTTGGAAATGTTATGCGCTCTGCCGGCTTTTTGG

upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
lower sequence: Vv02s0025g03530.t01 (Vitis vinifera), 3'ss of exon 11
gtttacccttttatctgtttacacgatggcatatctgtcgttgctaggtatcgcaataactcttgtcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
|| ||  |   |     |  |   ||||  || | | |  ||  ||| | | |  |         | |  |   || | | | ||||| ||||| ||||| ||| | || ||||| ||||||||||| || || |||||||| || ||||| ||||| |||||||||
gtataggcacctgag-atcaaattgatgaaat-tttatatttcttagatgttgtcacctaagaaatatgttattttttccattcagGTCAGGCTGAAGAGATACTTGGAAATGAGGGGTGCTGATGGAGGGCCCTGGAGGAGGTTATGTGCTTTGCCAGCATTTTGG

upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S28_268V6.1 (Physcomitrella patens), 3'ss of exon 10
--------gtttacccttttatc-tgtttacacg-atggcatatctgtcgttgctaggtatcgcaataactcttgtct-tctgcattctgcttgc---agGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
         ||  |   | |||  | |||  ||   |||     |||  || | |   | |  ||      |   |   | ||  ||||  ||||   |||| ||  | ||  ||||| | |||||||| || ||||||||||| |||||| |  |||||||||| ||||||||||| |||
cttcgtaacttggcttctatatggtttttggacttgtggtgatcctgctgtaggttaatgttacataggtacggattgatatgacttctctttgctgcagGTGAGATTGAAACGGTACTTAGAGATGAGGGGAGCTGATGGTGGTCCATGGCGCCGATTGTGTGCTTTGCCTGCATTCTGG

upper sequence: GRMZM2G111579_T01 (Zea mays), 3'ss of exon 10
lower sequence: PP1S479_14V6.1 (Physcomitrella patens), 3'ss of exon 10
-------------------------------------------------------------------------------------------------------gtttaccct-tttatc-tgtttacacg-atggcatatctgtcgttgctaggtatcgcaataactcttgtcttctg---cattctgctt--gcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
                                                                                                       |     | | |||||  ||| || |    |  ||    ||  ||||   |  ||     ||  | |    |  ||   |||  |  ||  |||||| ||||||||  | ||  | |||||||| || ||||||||||| |||||| |  |||||||||| |||||||||||||||
gtttctagtcattttgtatttcccgtctaatctttgaatacatggataattatagtgagcaatgctcgattctacaagaaatctcttaccattgtactgaattgcccggcttatttattgtgtctagatttgtttcagtcttgctgttggcggacattatg-tacgtgtaaattgatggagcatcatttttccgcagGTGAGGCTAAAACGTTATTTGGAGATGAGGGGAGCTGATGGTGGTCCATGGCGACGATTGTGTGCATTGCCTGCATTTTGG

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|211306284|gb|FL001397.1|FL001397
EST:     TGCCCACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG                         GTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCCACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAGgtttaccctt ... ctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGG
EST: gi|211304265|gb|FL001391.1|FL001391
EST:     TGCCTACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAG                         GTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGG
genomic: TGCCCACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAGgtttaccctt ... ctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGG

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: 312

GATTTTATGCAAGGAAAGCTTCCACAGGCTCCTGGGGAGTTGCCCACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAGgtttaccctt ... ctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 872

GATTTTATGCAAGGAAAGCTTCCACAGGCTCCTGGGGAGTTGCCCACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAGgtttaccctt ... ctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1782

GATTTTATGCAAGGAAAGCTTCCACAGGCTCCTGGGGAGTTGCCCACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAGgtttaccctt ... ctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG


Block sizes: 49 (upstream exon), 39 (downstream exon)
Score: 188

GATTTTATGCAAGGAAAGCTTCCACAGGCTCCTGGGGAGTTGCCCACTCTTAACGATTGGGAGAACCATCTAACAACAATTTTTCCTGAGgtttaccctt ... ctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgtcgttgctaggtatcgcaataactcttgtcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG
                      caataac  putative branch site (score: 188)
                                           ttctgctt  putative PPT
                       aataact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttacccttttatctgtttacacgatggcatatctgtcgttgctaggtatcgcaataactcttgtcttctgcattctgcttgcagGTTAGGCTAAAGAGGTACCTTGAGATGAGAGGTGCTGATGGTGGCCCATGGAGGAGATTGTGTGCGTTGCCTGCATTTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT