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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattactcttcctaattttgattgatattttaatttttgactgattttttggtccatccctaaggaagtcaataccatgctgtaaatcttggttttgattgttatttgcaaactaataaaccctctggccttgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG

Basic information

species Zea mays
transcript GRMZM2G002687_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g35570.3 (Oryza sativa), 3'ss of exon 3
gtaagattactctt---cctaattttgattgatattttaatttttgactgattttttggtccatccctaaggaagtcaataccatgctgtaaatcttggttttgattgttatttgcaaactaataaaccctctggccttgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG
||||| ||  ||||     || | |||||| || ||| | ||| ||||| ||||  ||  |  | | |  |  |  |||         |||| |||||   || |||  ||||    |   ||  || |||||| | || ||| ||||||||||||||||||||||| |  |||||||||||||||| ||    ||||||
gtaaggttcttcttaactgtagtcttgatttatctttca-tttatgactaatttaatga-ctgttcttctgctaagcaa---------gtaattcttgagatttatt--tattctatagaaaagtaatcctctgtcattttcttacagTGCTTTTTATGAAAACATGGTTAAAGTTGCCAGATGTGTGACATATAATAAG
















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|67015552|gb|CO444301.1|CO444301
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|148959767|gb|EC905658.2|EC905658
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGATAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|67037924|gb|CO464466.1|CO464466
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|6020814|gb|AW065742.1|AW065742
EST:     ATTCATTTTCTCTGATTTTTCTTTTGNTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: ATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|149010069|gb|EE041876.2|EE041876
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|71305908|gb|DR789081.1|DR789081
EST:     TTGACATTTGAA-GAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTGACATT-GAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|148935574|gb|EC879617.2|EC879617
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGA
EST: gi|149105517|gb|EE291042.2|EE291042
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|9953035|gb|BE639618.1|BE639618
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGCTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|91049846|gb|EB160264.1|EB160264
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|211139771|gb|FL315903.1|FL315903
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|149073834|gb|EE162156.2|EE162156
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|67014073|gb|CO442822.1|CO442822
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
EST: gi|148973279|gb|EE024361.2|EE024361
EST:     TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGG                         TGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA
genomic: TTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAA

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: 94

AAAGTAAAAGGCTTGCCCGTGAAAATGCTAAAGATATTATAGCATGTGGTTTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

AAAGTAAAAGGCTTGCCCGTGAAAATGCTAAAGATATTATAGCATGTGGTTTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 145

AAAGTAAAAGGCTTGCCCGTGAAAATGCTAAAGATATTATAGCATGTGGTTTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

AAAGTAAAAGGCTTGCCCGTGAAAATGCTAAAGATATTATAGCATGTGGTTTTGACATTGAAAGAACATTCATTTTCTCTGATTTTTCTTTTGTTGGAGGgtaagattac ... tgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttggttttgattgttatttgcaaactaataaaccctctggccttgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG
                        aactaat  putative branch site (score: 151)
                                          ccttgtctc  putative PPT
      ttttgattgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattactcttcctaattttgattgatattttaatttttgactgattttttggtccatccctaaggaagtcaataccatgctgtaaatcttggttttgattgttatttgcaaactaataaaccctctggccttgtctcacagTGCTTTTTATGAAAACATGATGCAAGTTGCCAGATGTGTAACTATGAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG