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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatatgtgcaatgagcttctcaatctttattatgcatccttttttaatctgacatatatttgaggtgtggatactatctctgcttatcaatatgctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT

Basic information

species Zea mays
transcript GRMZM2G112337_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G112337_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 5
gtaaatatgtgcaatgagcttctcaatctttattatgcatccttttttaa---tctgacatatatttgaggtgtggatactatctctgcttat-caatatgctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT
|||| | |   ||| |||| |||   ||||  | || || || |||||     ||||  | ||| |  |    |||||| ||| | || |||     |||| |||||||||||||||||||||||||||||||| |||||||||||||| |||||||  |  |||  || || |  |||| ||||   || || |||||||  || ||||
gtaattcta--caacgagcctcttgttcttactcatccaaccctttttgtatctctgtaacatagtacatcc-tggatattatttatgattaaatgctatg-tttctcagATTCAAGCTCTAGCTTCCCAGCTAACTGATCTTTGGAACCTAATGGACACCTCTGCTGATGAGCGACAACTTTTTGACCATGTCACATGCAACATTTCCT
















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|76013335|gb|DT940505.1|DT940505
EST:     TAAAATGGTGATTGTAC-TGAAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: TAAAATGGTGATTGTACTTG-AAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|149015046|gb|EE044792.2|EE044792
EST:     AAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTT-GAACTTTAATGGATTC
genomic: AAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAAC-TTAATGGATTC
EST: gi|76015436|gb|DT942606.1|DT942606
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|148928684|gb|EC873287.2|EC873287
EST:     AGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTT-GAACTAAATGGATTCT
genomic: AGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|211422903|gb|FL467603.1|FL467603
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|71763124|gb|DR961061.1|DR961061
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|76289490|gb|DV029058.1|DV029058
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|67014008|gb|CO442757.1|CO442757
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|71324223|gb|DR798814.1|DR798814
EST:     CTAAAATGGTGATTGTACTTG-AGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|149100804|gb|EE186898.2|EE186898
EST:     GTGATTGTAC-TGAAGAAGAAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: GTGATTGTACTTGAAGAAG-AAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|74246102|gb|DT654016.1|DT654016
EST:     GAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATC-TTGGGACTTTAATGGATTC
genomic: GAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAAC-TTAATGGATTC
EST: gi|76015435|gb|DT942605.1|DT942605
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|78112667|gb|DV531061.1|DV531061
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|76013336|gb|DT940506.1|DT940506
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|149088740|gb|EE177864.2|EE177864
EST:     GAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: GAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|148947543|gb|EC893016.2|EC893016
EST:     AATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: AATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|148999824|gb|EE036848.2|EE036848
EST:     AATGGTGATTGTACTGGAAGAGGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: AATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|149098529|gb|EE184515.2|EE184515
EST:     GAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: GAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|148933839|gb|EC877798.2|EC877798
EST:     AAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: AAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|211422902|gb|FL467602.1|FL467602
EST:     CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: CTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
EST: gi|78112666|gb|DV531060.1|DV531060
EST:     AAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGG-TTGCAAAG                         ATTTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTC
genomic: AAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagA-TTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTC
EST: gi|149096272|gb|EE181982.2|EE181982
EST:     TAAAATGGTGATTGTAC-TGAAAGAAGAAAAATCGAAGAGGTTGGCAAAG                         ATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT
genomic: TAAAATGGTGATTGTACTTG-AAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCT

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: 96

TGTTGGTGTCCAATCCAAGAGCATTAGTGGCGAAACAATATCCAAGCTGTCTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 44

TGTTGGTGTCCAATCCAAGAGCATTAGTGGCGAAACAATATCCAAGCTGTCTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT


Block sizes: 46 (upstream exon), 44 (downstream exon)
Score: 43

TGTTGGTGTCCAATCCAAGAGCATTAGTGGCGAAACAATATCCAAGCTGTCTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 35

TGTTGGTGTCCAATCCAAGAGCATTAGTGGCGAAACAATATCCAAGCTGTCTAAAATGGTGATTGTACTTGAAGAAGAAAAATCGAAGAGGTTTGCAAAGgtaaatatgt ... gctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgacatatatttgaggtgtggatactatctctgcttatcaatatgctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT
                                            tgctttctc  CT-rich tract
     atatatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatatgtgcaatgagcttctcaatctttattatgcatccttttttaatctgacatatatttgaggtgtggatactatctctgcttatcaatatgctttctcagATTCAAGCTCTAGCTTCCCAGCTATCTGATCTTTGGAACTTAATGGATTCTCCTGTGGAGGAACAGCAACCTTTTCGTCACGTAACATGCATAATGTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA