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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatccttgtagtttccatatgtcttctgttttcccgtgcttcatgatgcaatagtttattagtaccgacatggcactaacgataaagaggatgcttgtaatgcag

Basic information

species Zea mays
transcript GRMZM2G052630_T01
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 9
lower sequence: LOC_Os05g03480.4 (Oryza sativa), 5'ss of exon 10
CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatccttgtagtttccatatgtcttctgttttcccgtgcttcatgatgcaatagtttattagtaccgacatggcactaacgataaagaggatgcttgtaatgcag
 ||||| ||||| ||||| |||||||||||||| |   |||| |||||||| || || |||||||| || ||||||||||||||||||||||||||||||||| ||||  | |  |   | || | | |||||||  | || |||  | ||||| | ||| |||  |      ||| || ||| ||||  ||    ||| ||||||||
TCCTATCGGCCTCATGCAAGCATGCCTTGATGTAGCTGTTCCTTATGTTCGCCAAAGAGAGCAATTTGGCCGTCCAATTGGTGAATTTCAGTTCATACAGgtatatccaggaaactcttacatatgtcctgttttatcctgtttctaggtgcaacattttgttaacagacgtctggtaccaaccataacaagttatcttttaatgcag

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA12G07570.1 (Glycine max), 5'ss of exon 11
CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatccttgtagtttccatatgtcttctg---ttttcccgtgcttcatgatgcaatagtttattagtaccgac-atggcactaacgataaagaggatgcttgtaatgcag
 ||| ||||  ||||||||||||| ||||||||||| ||||| |||||||||||  | ||||| || || ||||| ||||| || |||||||| ||||||||   | ||| |      ||| ||| || ||   || ||| | | |   |  |  |   ||   | | |     | ||  || |  |  |      |||  |||   | |||
TCCTCTTGGTATTATGCAGGCATGTCTTGATGTTGTCCTTCCTTATGTTCGACAACGAGAGCAGTTTGGTCGTCCTATTGGGGAGTTTCAGTTTATACAGgt---ttcttatgcacaacat-tgttttttgcaattatcctgcg-tgtgtattttatgtgtacgtgaatcttagccatcacattttcattt-----gatctttg-gttacag

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 9
lower sequence: GLYMA11G15900.1 (Glycine max), 5'ss of exon 11
CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatccttgtagtttccatatgtcttctgttttcccgtgcttcatgatgcaatagtttattagtaccgac-atggcactaacgataaagaggatgcttgtaatgcag
 ||| ||||  ||||||||||||| |||||||| || ||||| |||||||||||  | ||||| || || ||||| ||||| || |||||||| ||||||||  ||  || ||     ||||| | ||    ||  ||    |   || |  |    | | | | |     | ||  || |  | ||      |||  |||   | |||
TCCTCTTGGTATTATGCAGGCATGTCTTGATGTCGTCCTTCCTTATGTTCGACAACGAGAGCAGTTTGGTCGTCCTATTGGGGAGTTTCAGTTTATACAGgtttattattatacacatcatattttttgcaattatcctgcatatgtgttttatgtttatgtgaatcttagccatcacattgtcaatt-----gatctttg-gttacag

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 9
lower sequence: AT3G45300.1 (Arabidopsis thaliana), 5'ss of exon 11
CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatccttgtagtttccatatgtcttctgttttcccgtgcttcatgatgcaatagtttattagtaccgacatggcactaacgataaagaggatgcttgtaatgcag
 ||  | ||  | |||||||||||||| ||   ||| ||||| ||| |||| ||||| || ||||| || |||||| |||| ||||||||||| ||||||||  | | |  |  |  || | |       |||| |   |   |||   |  |||    ||  | | |  | |     ||   ||     ||                
GCCCTTAGGGATCATGCAGGCATGCCTCGACAATGTTCTTCCCTATATTCGCCAGAGAGAACAATTTGGTCGTCCAGTTGGGGAATTTCAGTTTATACAGgttgagcttgatcat--ccttctcataaacgtttccgaatatctcaaactttaatca--taagattcctaaaacaattctgttgaatttcag----------------

upper sequence: GRMZM2G052630_T02 (Zea mays), 5'ss of exon 9
lower sequence: Vv06s0004g03140.t01 (Vitis vinifera), 5'ss of exon 11
CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatccttgtagtttccatatgtcttctgttttcccgtgcttcatgatgcaatagtttattagtaccgacatggcactaacgataaagaggatgcttgtaatgcag
 ||  |||| ||||||||||||||  | ||||| || ||||| |||||||| ||||| || || || || ||||||||||| ||||||||||| ||||||||  ||  ||     |     | || |||| | |     || |    ||| |    ||| |  |||  |      || || ||  |          ||   ||| |||
GCCCCTTGGTCTTATGCAGGCATGTATAGATGTAGTTCTTCCCTATGTTCGGCAGAGAGAACAGTTTGGCCGTCCAATTGGAGAATTTCAGTTTATACAGgtccataattcgtaatcatgcaagttttctatctaatgttgttattcgatacctgtgttga--agtttca-----gctcttacactgttagttgacctgaaaatacag

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|24769404|gb|CA404533.1|CA404533
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|110190881|gb|EC872779.1|EC872779
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|31354622|gb|CD438979.1|CD438979
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|78105056|gb|DV523474.1|DV523474
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|31360769|gb|CD445126.1|CD445126
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|60347547|gb|DN214520.1|DN214520
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|78027006|gb|DV495393.1|DV495393
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|5108421|gb|AI740134.1|AI740134
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|74240406|gb|DT648320.1|DT648320
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|76936507|gb|DV174755.1|DV174755
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|50336352|gb|CO531478.1|CO531478
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|78124549|gb|DV542933.1|DV542933
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|110525230|gb|EE029414.1|EE029414
EST:     GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: GACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
EST: gi|149076167|gb|EE164757.2|EE164757
EST:     TTTCAGTTCATACAG                         GGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG
genomic: TTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG

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), 41 (downstream exon)
Score: 59

CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 368

CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 237

CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG


Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 69

CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatcctt ... tgtaatgcagGGGAAAATGGCTGATATGTACACCTCATTGCAGTCATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCTATTGGCCTTATGCAGGCATGCCTTGATGTTGTACTTCCATATGTTCGACAGAGGGAGCAATTCGGGCGTCCAATTGGTGAATTTCAGTTCATACAGgtaaatccttgtagtttccatatgtcttctgttttcccgtgcttcatgatgcaatagtttattagtaccgacatggcactaacgataaagaggatgcttgtaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA