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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgtaccttatgagtgaacattgcag

Basic information

species Zea mays
transcript GRMZM2G119773_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G119773_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g56970.2 (Oryza sativa), 5'ss of exon 4
ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggt-ttctcccctttcctgctctaacttatctgcaaattgttatcatgtaccttatgagtgaacattgcag
|||||||||||  |||||||||| ||||||||||||||| ||||| |||||||||||||| |||||||| ||||| |||||||||||||| || || |||||  ||  | ||||   || | ||||| |||||| |   || |   |  |||| |         |  ||| ||||||
ATTAGATGTTGTTGATGAAAACACGCCCTTGCAAGATGCGTTTCTTCTTGCAGATGATGTTCTTCGTCAAGGTGTCCAAGGAATATCAGATATTATTACAgtaagtattcttcttatctatgctgctgtaacttgtgatcacacaatactcatct---------gaaaactttgcag
















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|148970650|gb|EE021357.2|EE021357
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCAT
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCAT
EST: gi|148940468|gb|EC885267.2|EC885267
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
EST: gi|211174836|gb|FL413961.1|FL413961
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAA
EST: gi|76923027|gb|DV169298.1|DV169298
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
EST: gi|211392485|gb|FL384044.1|FL384044
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
EST: gi|148941071|gb|EC885931.2|EC885931
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTT
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTT
EST: gi|149097959|gb|EE183902.2|EE183902
EST:     AGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCANCA                         -TACCGGGACTTTGTCA-TGTTGATTTTGCTGATGTAAAAGCTGTCATGA
genomic: AGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCA-CAgtgggtggtt ... aacattgcagATACCGGGACTT-GTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGA
EST: gi|149097351|gb|EE183189.2|EE183189
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
EST: gi|60356845|gb|DN223818.1|DN223818
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
EST: gi|78078489|gb|DV506902.1|DV506902
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
EST: gi|211478791|gb|FL377823.1|FL377823
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAA
EST: gi|148971012|gb|EE021841.2|EE021841
EST:     CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACA                         ATACCGGGACTTGTCCNATGT-GATTTTGCTGATGTAAAAGCTGTCATGAA
genomic: CAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCA-ATGTTGATTTTGCTGATGTAAAAGCTGTCATGAA

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: 263

ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 131

ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 86

ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 123

ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtt ... aacattgcagATACCGGGACTTGTCAATGTTGATTTTGCTGATGTAAAAGCTGTCATGAAAAACTCTGGAACTGCCATGCTCGGTGTTGGTGTTTCTTCCAGCAAAAATC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTAGATGTTGCGGATGAAAACATGCCCTTGCAAGATGCATTTCTCCTTGCAGATGATGTCCTTCGTCAGGGTGTTCAAGGAATATCAGACATCATCACAgtgggtggtttctcccctttcctgctctaacttatctgcaaattgttatcatgtaccttatgagtgaacattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA