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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatttgacctgtttttgcatgtagattgacagtactactggagtagcttttattacatacataatacatacccctcttgttatcgtttttacacaaaaaaactgatacattcgtatggatgtatctctacttctgattgttgcag

Basic information

species Zea mays
transcript GRMZM2G066051_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G066051_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g39630.1 (Oryza sativa), 5'ss of exon 2
AGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaa-tttgacctgtttttgcatgtagattgacagtactactggagtagcttttattacatacataatacatacccctcttgttatcgtttttacacaaaaaaactgatacattcgtatggatgtatctctacttctgattgttgcag
 || ||||| ||||| || || || ||||||||||||||||||||||| |||||||||||||||||  |||| ||   |||||| ||| | || || |||||||| || |||    ||||||||   || ||||| |  |  ||||||         |  |||||  |       |   | | ||| ||  ||||       | |   || |   |||   |||||| ||||| | |               
TGAACCTGTGACTGAGGCTTGCGTGCAATTGACCCAAGAATTCTTCAGAGAGAACACTTTACGGCTTCTAATTATTTGTCTTCCGAAATTGAACTTAGAGgtatgcaactttattttgtttttg---gtggattg-cgatggtactgg---------tgatacatgtac------tgttcttattgctactgttt-------agatggctaacttattttaatggatatatct-tgcag-------------
















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|149041352|gb|EE046990.2|EE046990
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|148999214|gb|EE036133.2|EE036133
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|78107219|gb|DV525637.1|DV525637
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|149072876|gb|EE161132.2|EE161132
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|7844268|gb|AW787490.1|AW787490
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|6194845|gb|AW146949.1|AW146949
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|211268420|gb|FL369229.1|FL369229
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|71447694|gb|DR828744.1|DR828744
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|148955827|gb|EC901514.2|EC901514
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|71328881|gb|DR801123.1|DR801123
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|31354689|gb|CD439046.1|CD439046
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|60340162|gb|DN207135.1|DN207135
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|32856027|gb|CD995708.1|CD995708
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTCGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|149082296|gb|EE171481.2|EE171481
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|6994177|gb|AW453391.1|AW453391
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|7844267|gb|AW787489.1|AW787489
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGTTTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGT
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATG-CTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGT
EST: gi|6022524|gb|AW067557.1|AW067557
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|6194848|gb|AW146952.1|AW146952
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|149079796|gb|EE168794.2|EE168794
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
EST: gi|149013854|gb|EE043335.2|EE043335
EST:     AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAG                         ACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA
genomic: AGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTA

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: 234

AGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 336

AGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

AGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 303

AGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatt ... attgttgcagACTAGGAAAGATGCTACTCAAGTTGTTGCAAACTTGCAAAGACAGCAAGTATCCTCAAAGATAGTAGCGTCTGAGTACCTAGAGTCAAATAAAGATCTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGCCTGTAACTGAAGCATGTGTACAATTGACCCAAGAATTCTTCAGGGAGAACACTTTACGGCTATTAATCATACATCTTCCAAAACTAAATTTGGAGgtatgtaatttgacctgtttttgcatgtagattgacagtactactggagtagcttttattacatacataatacatacccctcttgttatcgtttttacacaaaaaaactgatacattcgtatggatgtatctctacttctgattgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG