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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacaactgaaactcctccatggcagccataagatgactgtgctattggtatcttatattattgtgattgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG

Basic information

species Zea mays
transcript GRMZM2G005308_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os11g04200.1 (Oryza sativa), 3'ss of exon 6
----------------gtatgacaactgaaactcctccatggcagccataagatgactgtgctattggtatcttat-attattgtgattgtt-catcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
                ||   | |||   ||||| |  |||  | | ||||  | |   ||   ||| | |||||   ||||    ||| || || |||||||||| ||||||||||||||||||||||||||| ||||||
gtatacttttaatcttgtccaataac-ataactcattgatgataacaataac-taatcatgtatttgttgtcttaccgttatcaatattatttcaacagGATGAAAGTAAGAGCAAGAAGGGTCTTGCTGAACTATATGAG

upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os12g04010.1 (Oryza sativa), 3'ss of exon 6
----------------gtatgacaactgaaactcctccatggcagccataagatgactgtgctattggtatcttat-attattgtgattgtt-catcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
                ||   | |||   ||||| |  |||  | | ||||  | |   ||  |||| | ||||    ||||    ||| || || ||||| |||| ||||||||||||||||||||||||||| ||||||
gtatacttttagtcttgtccaagaac-ataactcattgatgataacaataac-taatcatgtaattgttgtcttgccgttatcaatattatttcaacagGACGAAAGTAAGAGCAAGAAGGGTCTTGCTGAACTATATGAG

upper sequence: GRMZM2G005308_T01 (Zea mays), 3'ss of exon 8
lower sequence: Vv17s0000g08620.t01 (Vitis vinifera), 3'ss of exon 6
----------gtatgacaactgaaactcctccatggcagccataagatgactgtgctattggtatcttatattattgtgattgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
           | |   ||    ||||  | | | |    | |   ||| |  |   |||  ||||     ||    |||   ||   |||||||||| ||||||||||||||||||||||||  | ||||||
gtaagcattttttttttaaaaacaactaattctttgtcatc-tgtaatgtccatctaatttttatccaccttttccttgacacttg--cagGATGAAAATAAGAGCAAGAAGGGTCTTGCTGAGATTTATGAG

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|60347217|gb|DN214190.1|DN214190
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|31363813|gb|CD448168.1|CD448168
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|24769907|gb|CA405036.1|CA405036
EST:     AAAGCTCCAAAGGAGCCCAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|60394413|gb|DN227283.1|DN227283
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|71764578|gb|DR962515.1|DR962515
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|31351205|gb|CD435562.1|CD435562
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAACAGCAAGAAGGGTATTGCTGAACT
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACT
EST: gi|71761969|gb|DR959906.1|DR959906
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|211183291|gb|FL434311.1|FL434311
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|31364214|gb|CD448569.1|CD448569
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGACCTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|211462204|gb|FL207481.1|FL207481
EST:     GCTCCAAAGGAGCACAAGGAACTG                         GATGAAMCTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: GCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|76011806|gb|DT938976.1|DT938976
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|40303495|gb|CK347882.1|CK347882
EST:     AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTG                         GAT-AAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
EST: gi|37392792|gb|CF633649.1|CF633649
EST:     AAGGAGCACAAGGAACTG                         GATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
genomic: AAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG

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: 100

AGTCATTTTGATGATGTTGAGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 87

AGTCATTTTGATGATGTTGAGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 79

AGTCATTTTGATGATGTTGAGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 44

AGTCATTTTGATGATGTTGAGAAGCCGTCTCTCTTGCCATCTAAAGCTCCAAAGGAGCACAAGGAACTGgtatgacaac ... tgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagccataagatgactgtgctattggtatcttatattattgtgattgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG
                          tatcttatattattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacaactgaaactcctccatggcagccataagatgactgtgctattggtatcttatattattgtgattgttcatcagGATGAAACTAAGAGCAAGAAGGGTCTTGCTGAACTGTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG