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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttttttccttttgtttactagcataatactgccaatcacaagtgcaggatgctctcttttgtttgtttatttgaaattttcttggggatgtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG

Basic information

species Zea mays
transcript GRMZM2G013890_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g58020.2 (Oryza sativa), 3'ss of exon 13
gttttttccttttgtttactagcataatactgccaa--tcacaagtgcaggatgctctcttttgtttgtttatttgaaattttcttggggatgtt-tttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG
   |  |  | || |    || | |  || |||||   |  ||  |||   ||  | |||   ||||||| |||| |  | ||  || || |||| ||| |||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||||  ||||| || 
--ataattttgttataatataaccttttattgccagagtttcatctgctacatcttatctgcggtttgttgattt-atttattgctgcggctgttatttgcagGTTCGCATGGCTGTATTCAATCAACACCATGTTGATGGGCTTGATTTAACAGTGAACCCCCTTTTGTACATGATGAGATGCTACCCT
















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|211429010|gb|FL174619.1|FL174619
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|211429009|gb|FL174618.1|FL174618
EST:     AACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: AACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|60343993|gb|DN210966.1|DN210966
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|32930219|gb|CF035031.1|CF035031
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|71307301|gb|DR789831.1|DR789831
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|60341793|gb|DN208766.1|DN208766
EST:     AACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: AACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|12970170|gb|BG266849.1|BG266849
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|22552549|gb|BU102388.1|BU102388
EST:     AGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: AGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|60352803|gb|DN219776.1|DN219776
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|76914779|gb|DV165687.1|DV165687
EST:     CAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: CAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|211429008|gb|FL174617.1|FL174617
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGTATCATGTTGATGGGCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|67015572|gb|CO444321.1|CO444321
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|78544243|gb|DV621741.1|DV621741
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|84980921|gb|DW531270.1|DW531270
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|5108202|gb|AI739915.1|AI739915
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|40336236|gb|CK370306.1|CK370306
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|211429006|gb|FL174615.1|FL174615
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|60349362|gb|DN216335.1|DN216335
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|71307303|gb|DR789832.1|DR789832
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|32932155|gb|CF036967.1|CF036967
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|211429007|gb|FL174616.1|FL174616
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|32932545|gb|CF037357.1|CF037357
EST:     TTTCTGGGGATCTGCAACCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTTAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|86472924|gb|DY239294.1|DY239294
EST:     TTTCTGGGGATCTGCAACCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|37390519|gb|CF632491.1|CF632491
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|211429005|gb|FL174614.1|FL174614
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|20802514|gb|BQ293564.1|BQ293564
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
EST: gi|37377213|gb|CF625190.1|CF625190
EST:     TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAG                         GTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG
genomic: TTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACG

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: 48 (upstream exon), 47 (downstream exon)
Score: 196

TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 174

TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 129

TGGTTGGTCCTAATGGCATTGGCAAGTCCACTATACTGAAACTAATTTCTGGGGATCTGCAGCCAACTTCTGGAACAGTATTTCGCTCTCCCAAGgtgcttcatt ... gtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggatgctctcttttgtttgtttatttgaaattttcttggggatgtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG
                                            tgttttt  CT-rich tract
            ttttgtttgtttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttccttttgtttactagcataatactgccaatcacaagtgcaggatgctctcttttgtttgtttatttgaaattttcttggggatgtttttacagGTTCGCATGGCTGTATTCAATCAGCATCATGTTGATGGCCTTGATTTGACGGTGAATCCCCTTTTGTACATGATGAAGTGCTATCCG

- - - - -ttttgtt
- - - - - - - - - - - - - -tactgcc
- - - - - - - - - - - - - - - - - -atcacaa
- - - - - - - - - - - - - - - - - - - - - gtgcagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttcttg