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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtcttttgtgtctgtcttcttgtttctgtcatttcataattcatttttgggatgttgacttctagaatttagagtttccttttttttaaatccttgcagctgcagttagaattcataaattcagtatccaaataaccacatgtcaaattttgtgtaacag

Basic information

species Zea mays
transcript GRMZM5G862931_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862931_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g40790.1 (Oryza sativa), 5'ss of exon 4
GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtcttttgtgtctgtcttcttgtttctgtcatttcataattcatttttgggatgttgacttctagaatttagagtttccttttttttaaatccttgcagctgcagttagaattcataaattcagtatcca-aataaccaca-tgtcaaa--ttttgtgtaacag
|||||||||||||||||||||||| | || ||||| |||||||| || || || ||||||||||||||||||||||||||||||||||||||||||||    |      |||  || | ||| |  |||||  |  |||| |    | || | || ||||      |    |||  |  || | ||||   |    ||  |  |  |   || ||    |  | ||| |||||| | | |||||||  |||  || | |||
GTTATTGATGCAAAAAACTTCAGGCTGCAAATTGATGAGCACAATAAGTCATCATCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttggtcctcag---tgttatcctatttgtaccattttgtc-ttcactac-agaatttggaattctttgtgctga--ttttgtggttctgaaatttgtcttacttga--tgaatcccaaaatgcaaacaaccataataacaaaagtgtcaaaactttcctggaccag

upper sequence: GRMZM5G862931_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g40404.1 (Oryza sativa), 5'ss of exon 5
GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtcttttgtgtctgtcttcttgtttctgtcatttcataattcatttttgggatgttgacttctagaatttagagtttccttttttttaaatccttgcagctgcagttagaattcataaattcagtatcca-aataac--cacatgtcaaattttgtgtaacag
|||||||||||||||  ||||||| | || ||||| ||||||||||| || || ||||||||||||||||||||||||||||||||| ||||||||||    |||    |||  || | ||| |  |||||  |  ||    |     || | || | ||     ||    ||    | |  | ||||   | | ||||    |  | | || ||    |  | ||| ||||||   |   |||||| |||   ||||||
GTTATTGATGCAAAAGCCTTCAGGCTGCAAATTGATGAGCACAAAAAGTCATCATCATTCCCTGAAGCATTTCATCAAATTGCATTTTCGgtaacttggtccttgg---tgttatcatatttgtaccattttgtctttg--ctacaaaatttggaatcctttgtgttga--ttctgctgtgctgaaatttgtcctgctga---tgaattccaaaatgcaaacaaccataataacagaaagcgtcaaactttccttaacag
















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|40336013|gb|CK370083.1|CK370083
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|78108723|gb|DV527141.1|DV527141
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|211125209|gb|FL458514.1|FL458514
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|76926513|gb|DV170904.1|DV170904
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|71435591|gb|DR816641.1|DR816641
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAACATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|50335360|gb|CO530486.1|CO530486
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|89760831|gb|DY689083.1|DY689083
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|71434868|gb|DR815918.1|DR815918
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
EST: gi|71446369|gb|DR827419.1|DR827419
EST:     ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCG                         GATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT
genomic: ACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGAT

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: 116

GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGATCTGGAAAAACATATTCGTGATGTGAATGCTCTGGTTACAGTGGTGCGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGATCTGGAAAAACATATTCGTGATGTGAATGCTCTGGTTACAGTGGTGCGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 126

GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGATCTGGAAAAACATATTCGTGATGTGAATGCTCTGGTTACAGTGGTGCGGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 133

GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtc ... tgtgtaacagGATGTTGTGATATTGAACAAAATTGACCTAGTGGAAGACAGTCTTGAGGATCTGGAAAAACATATTCGTGATGTGAATGCTCTGGTTACAGTGGTGCGGT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTATTGATGCAAAAAACTTCAGGGTTCAGATTGACGAGCACAAAAACTCTTCCTCATTCCCTGAAGCATTTCATCAAATTGCATTTGCGgtaacttgtcttttgtgtctgtcttcttgtttctgtcatttcataattcatttttgggatgttgacttctagaatttagagtttccttttttttaaatccttgcagctgcagttagaattcataaattcagtatccaaataaccacatgtcaaattttgtgtaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC