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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctcaactcatcaaagttatctgatattagcccattcttcactcagtttacattactgagacattgtacttgtgtttccacacag

Basic information

species Zea mays
transcript GRMZM2G134889_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134889_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g01010.1 (Oryza sativa), 5'ss of exon 8
GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctcaactcatcaaagttatctgatattagcccattcttcactcagtttacattactgagacattgtacttgtgtttccacacag
   || ||||| | |||||| || || ||||| ||||| |||||||| || ||||| || |||||||||||||||||         | | |||| ||||    |  | |||| |||| | | |||  || |||||||||     |||||| ||| ||||
AGATTTGCTGAGGATTTCTTAGAGGAAAAGCTCACACCGTTCTACAAGTCTGAACCTGTACCTGAATCTgtgagtct---------ataattatatgatg--ggttctttctccacttattgtaccataatgagacatt----ctgtgttcccatacag
















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|211193716|gb|FL465420.1|FL465420
EST:     ATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTG-TGTTTGGGAAGAATCTGGATCTAATAGT
genomic: ATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTG-TTGGGAAGAATCTGGATCTAATAGT
EST: gi|32165106|gb|CD670424.1|CD670424
EST:     CCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: CCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|149077066|gb|EE165722.2|EE165722
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|71767590|gb|DR965527.1|DR965527
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|110965155|gb|EE185055.1|EE185055
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|37392565|gb|CF633534.1|CF633534
EST:     TTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|31909789|gb|CD651094.1|CD651094
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|148938717|gb|EC883049.2|EC883049
EST:     AAAGACAAAGCTTACACCATTCTCCAAATCGGAACCAGTGCCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGT
genomic: -AAGAC-AAGCTTACACCATTCTACAAATCGGAACCAGTG-CCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGT
EST: gi|67020721|gb|CO449470.1|CO449470
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|32801735|gb|CD953971.1|CD953971
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCCGGATC
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATC
EST: gi|148974380|gb|EE025157.2|EE025157
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|76285047|gb|DV024615.1|DV024615
EST:     GGAAGACAAGCTTACACCATTCTACAAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: GGAAGACAAGCTTACACCATTCTAC-AAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|67013918|gb|CO442667.1|CO442667
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|211193717|gb|FL465421.1|FL465421
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT
EST: gi|78105578|gb|DV523996.1|DV523996
EST:     TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCT                         AATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATTTAATAGTT
genomic: TGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTT

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: 211

GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 196

GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctca ... ttccacacagAATGATGGGGATGTGAAAATTGTTGTTGGGAAGAATCTGGATCTAATAGTTTTTGATGAAACAAAAGATGTACTTCTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTCGCTGAAGGTTTCTTGGAAGACAAGCTTACACCATTCTACAAATCGGAACCAGTGCCTGAATCTgtgagtctcaactcatcaaagttatctgatattagcccattcttcactcagtttacattactgagacattgtacttgtgtttccacacag

- - - - - - - - -  TGGAAG
- - - - - - - - - - GGAAGA
- - - - - - - - - - - - - CAAGCT