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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtacttcatgtgaatgcttgatctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatag

Basic information

species Zea mays
transcript GRMZM2G389362_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G389362_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g02464.1 (Oryza sativa), 5'ss of exon 3
GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtacttcatgtgaatgcttgatctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatag
| |||||||| ||||| |||||||| || ||||||||||||||||||||| ||||||| ||||| ||||||||||||||||||||||||| || |||      |  |||||  ||  |||| | | ||| | | || | |||||||   | ||||| |  ||| ||| | |||
GTCTTGATCACAAAGCCATAGATAAGTGCATTGGTGATCCAGATGCTGATAAAGAAAATCCTGTGCTGAAAGCTGAACAGGATGCACAGgttactac-----atacatgct--ataattttctattcatacaactggtaatctgaatttagcatcacccaccattttatgtag

upper sequence: GRMZM2G389362_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 3
GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtacttcatgtgaatgcttgatctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatag
| |||||||| ||||| |||||||| || |||| |||||||||||||||| ||||||| ||||| ||||||||||||||||||||||||| ||||||      |  |||||  ||  |||| | | ||| | | || | |||||||   | || || |  ||| ||| |||||
GTCTTGATCACAAAGCCATAGATAAGTGCATTGCTGATCCAGATGCTGATAAAGAAAATCCTGTGCTGAAAGCTGAACAGGATGCACAGgttagtac-----atacatgct--ataattttctattcatacaactggtaatctgaatttaacaccacccaccattttatatag

upper sequence: GRMZM2G389362_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G14800.1 (Glycine max), 5'ss of exon 3
GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtacttcatgtgaatgcttgatctttttttgtc-catcctatt---gttgatctgaacacatcatca--tcatccactttgtatag--------------
|  |||||   || | |||  |  | ||| ||||  ||||   |||  |||  || ||||||||||| || ||||||||||||||||||| | ||  | || | | |    |  |   || |  |  ||| |||||   |||| |||       | || |   ||| |  || || ||               
GTGTTGATTTGAAGGAAATTAAAGATTGTGTTGGAAATCCTAGTGCAAATGCCGACAACCCTGTTCTTAATGCTGAACAGGATGCACAGgttggtcttacaggaggagaaattcttaattctgatggcattctattagggttgttcttgttctctaattaggccattctgttggtttatgactttggtttcag

upper sequence: GRMZM2G389362_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA09G41070.3 (Glycine max), 5'ss of exon 3
GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtacttcatgtgaatgcttg-atctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatag---------------------------------
|   |||||  ||    ||  |  | ||  |||| |||||  |||| |||| |||||| |||||||| || ||||||||||||||||||| | |   |  |    |||||    || ||||| ||     | | || ||  | |   ||  |   ||         || |||                                   
GTGCTGATCTGAAGAAGATTAAAGACTGCGTTGGAGATCCCCATGCAGATGTAGAAAATCCTGTTCTTAAGGCTGAACAGGATGCACAGgttggctttcta---aaatgcaaacatttttttatgctatccttgtttttttttttttcatttaggcaattctgttgttttatgagtgtattgtaattttttctaacttcggtttcag

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|67022369|gb|CO451118.1|CO451118
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211315830|gb|FK969313.1|FK969313
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313814|gb|FK969304.1|FK969304
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313816|gb|FK969306.1|FK969306
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313815|gb|FK969305.1|FK969305
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313819|gb|FK969309.1|FK969309
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|32937726|gb|CF042545.1|CF042545
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313813|gb|FK969303.1|FK969303
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|211313817|gb|FK969307.1|FK969307
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|6445395|gb|AW179463.1|AW179463
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCA
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCA
EST: gi|67026759|gb|CO455508.1|CO455508
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
EST: gi|32937931|gb|CF042750.1|CF042750
EST:     CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAG                         ATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT
genomic: CAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATT

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), 48 (downstream exon)
Score: 170

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG


Block sizes: 47 (upstream exon), 42 (downstream exon)
Score: 97

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 98

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtactt ... ctttgtatagATTGGCAAGGGCTCTCGTGGTGATGTTACCATCTTACCAACTCTGGTAATTAACAATAGACAATACAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTGATCATAAAGCAATAGATAAATGTATTGGTGATCCAGATGCTGATGAAGAAAACCCTGTTCTGAAAGCTGAACAGGATGCACAGgctagtacttcatgtgaatgcttgatctttttttgtccatcctattgttgatctgaacacatcatcatcatccactttgtatag

- - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG