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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcaattgatgactagcactgtttgtcccttcagctaggatgtattatcagtgatcatatttgtttcaattgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAATAATTATTTTTACCCCCATACTGAA

Basic information

species Zea mays
transcript GRMZM2G091560_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091560_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g34210.1 (Oryza sativa), 3'ss of exon 8
gtttgtcaattgatgactagcactgtttgtcccttcagc---taggatgtattatcagt--gatcatatttgtttcaattgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAA---TAATTATTTTTACCCCCATACTGAA
||||||| |||  ||| |  | |||||   |     |||   |    |  || | ||||   |||| |||  ||||||||| ||  |||||||||||||||| ||||| || || || || ||||||||||| ||||| || || |||||  | || |||||    | |     |||  |  || ||    
gtttgtctattc-tgattt-ctctgttccccatggtagcgtttgtcttacatcaacagtttaatcaaatt-atttcaattgtttccagGTGATGAAAGCATCAAAGGGTAAAGCTAATCCTGTTTTGTTGAACAAAATCCTCGGGGAGAAATTGAAGGCCAATAGTTGAGGGGGTTTGTCGACAAACG---
















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|211515148|gb|FL351622.1|FL351622
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAAT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAAT
EST: gi|78022483|gb|DV490870.1|DV490870
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|211486172|gb|FL326647.1|FL326647
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|4621448|gb|AI612281.1|AI612281
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|4647395|gb|AI622470.1|AI622470
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|5915470|gb|AW053111.1|AW053111
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|32797438|gb|CD949674.1|CD949674
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGTATTTTTTGCTGGCCAG                         GTGATGAAAGTATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAGTT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|5713973|gb|AI943958.1|AI943958
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|211183316|gb|FL321581.1|FL321581
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAAT-
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|32846860|gb|CD986541.1|CD986541
EST:     ACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: ACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|211362610|gb|FL353331.1|FL353331
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|32789262|gb|CD941498.1|CD941498
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|5929050|gb|AW056342.1|AW056342
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|211158667|gb|FL318097.1|FL318097
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCC
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCC
EST: gi|211031236|gb|FL345766.1|FL345766
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAATGCCAACCCAGTTTTGTTGAATAAA
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAA
EST: gi|211274217|gb|FL334363.1|FL334363
EST:     AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
EST: gi|94478769|gb|EB707727.1|EB707727
EST:     AGCAGTACCGTGCTGGAAAAAATAAGCTACAAGGATTTTTTGCTGGCCAG                         GTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT
genomic: AGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATT

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), 49 (downstream exon)
Score: 26

AATTGAGGCAATGGTAGATAAAGTAATTGCTGATAATCCAAAGCAACTTGAGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAATAATTATTTTTACCCCCATACTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

AATTGAGGCAATGGTAGATAAAGTAATTGCTGATAATCCAAAGCAACTTGAGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAATAATTATTTTTACCCCCATACTGAA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

AATTGAGGCAATGGTAGATAAAGTAATTGCTGATAATCCAAAGCAACTTGAGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAATAATTATTTTTACCCCCATACTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

AATTGAGGCAATGGTAGATAAAGTAATTGCTGATAATCCAAAGCAACTTGAGCAGTACCGTGCTGGAAAAACTAAGCTACAAGGATTTTTTGCTGGCCAGgtttgtcaat ... ttgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAATAATTATTTTTACCCCCATACTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcccttcagctaggatgtattatcagtgatcatatttgtttcaattgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAATAATTATTTTTACCCCCATACTGAA
                                           aattgat  putative branch site (score: 51)
                                atatttgtttcaattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcaattgatgactagcactgtttgtcccttcagctaggatgtattatcagtgatcatatttgtttcaattgattatagGTGATGAAAGCATCGAAGGGGAAGGCCAACCCAGTTTTGTTGAATAAAATTCTTGGAGAGAAGCTAAATGCCAAATAATTATTTTTACCCCCATACTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC