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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattatattataaattttcaaagataaaaattatgcatgagtttgattgcagaaatattataacaaaaaagtggcaattacaaatcaaatgtagagttctgttttttaataaaaaaaatcaaatatatgaatgtgagacatatttatgatgcatctgatgagtcatgacgatttgtctccttttgaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 3'ss of exon 7
gtgagtattatattataaattttcaaagataaaaattatgcatgagtttgattgcagaaatattataacaaaaaagtggcaattacaaatcaaatgtagagttctgttttttaataaaaaaaatcaaata---tatgaatgtgagacatatt-tatgatgcatctgat-gagtcatgacgatttgtctccttttg-aactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA
|| |||| |  |||  |   |||   |   | |  | |  |       | | | |||   |||| |  |   | |   | ||| | |||||  ||   || || |||     | |||| | |    |  |   ||||  | ||  |  |||    |||   |  |  | | | ||  | | ||  |||| ||    || | | ||| ||||| |||||||| || ||||| ||  ||||||| |||||||||||| |||| ||||||||||||||||||||   |||||||
gtaagtactgaattgca---ttttccattcagaggtcaaaccatcaccttactacaggcgtattgtctcttgagat--gtaatgagaaatctgatagtgacttgtgtgacaaattaaacatatcttaggacaatatggttctgtaatgtatcacttgacatagatatttgtgccaatatgcttattctctttgaataattcttagGGGAGTACCTGGCTTTGACCGGTGCAAGGTTGAATGCAAAGGAAATGATTGCTGCCGGTCTTGCTACTCATTTTGTTCCTTCTGAA
















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|33942681|gb|CF349281.1|CF349281
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|101390789|gb|EB817329.1|EB817329
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|71448792|gb|DR829842.1|DR829842
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|78109535|gb|DV527951.1|DV527951
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|149000045|gb|EE037146.2|EE037146
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|76292518|gb|DV032086.1|DV032086
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTTACTGTTGCTAGACTGAAT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAAT
EST: gi|74239820|gb|DT647734.1|DT647734
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|71304196|gb|DR788218.1|DR788218
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|60352184|gb|DN219157.1|DN219157
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|30052459|gb|AI065748.2|AI065748
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|32930057|gb|CF034869.1|CF034869
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|71429840|gb|DR810890.1|DR810890
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGGTTTTACTGGTGCTAGACTG
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTG
EST: gi|93012152|gb|EB637672.1|EB637672
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|91056953|gb|EB167371.1|EB167371
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     CAGATNGTAG-TTTTTCTACATCCCATTCCCGGCT-CCTGGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CAGATTGTAGCTTTTCCTACAT-CCATTCCCGGCTCCCT-GGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|149089063|gb|EE178226.2|EE178226
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|148959115|gb|EE010592.2|EE010592
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|71448491|gb|DR829541.1|DR829541
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCT
EST: gi|74238393|gb|DT646307.1|DT646307
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTACCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
EST: gi|71447954|gb|DR829004.1|DR829004
EST:     CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAG                         GCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT
genomic: CACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTT

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), 48 (downstream exon)
Score: 71

ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 197

ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 203

ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 215

ATCTTTGCTACTCCTGAGGCTAGTGTTGGATTGCACACAGATTGTAGCTTTTCCTACATCCATTCCCGGCTCCCTGGATATTTAGgtgagtatta ... gaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttatgatgcatctgatgagtcatgacgatttgtctccttttgaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA
             atctgat  putative branch site (score: 215)
                                tttgtctccttttg  putative PPT
                                         ttttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattatattataaattttcaaagataaaaattatgcatgagtttgattgcagaaatattataacaaaaaagtggcaattacaaatcaaatgtagagttctgttttttaataaaaaaaatcaaatatatgaatgtgagacatatttatgatgcatctgatgagtcatgacgatttgtctccttttgaactatcagGCGAGTATCTGGCTTTAACTGGTGCTAGACTGAATGCGAAGGAAATGATTTCTGCTGGTCTTGCTACTCATTTTGTCAGTTCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA