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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatctacataagggtccattataagttaattcttacatatcaagaactgttgtaacgagacctatgtctgctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG

Basic information

species Zea mays
transcript GRMZM2G149272_T04
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149272_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g42520.2 (Oryza sativa), 3'ss of exon 5
gtgagtatctacataagggtccattataagttaattcttacatatcaagaactgttgtaacgagacctatgtctgc-tgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG
|| ||| ||||||  ||| |    ||| |||||||     ||||| | ||| |||  ||   | ||  || ||| | ||| |||||| ||||||||||||||||| || ||||| || |  ||||| || ||||||||||||||||| |||||||||||||
gtaagtttctaca-gaggctatgctattagttaatgaaagcatattaggaaatgtaatatttatactcatatcttcctgacttagGTTGCTCAAGGTGCTAAGCTGCGCGGGGCTTCTATAATTATCGGTGTTGATACTAATCCTGAAAAGCAAGAAAAGG
















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|211510916|gb|FL028116.1|FL028116
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|71771533|gb|DR969470.1|DR969470
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|14203856|gb|BG837533.1|BG837533
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|148958260|gb|EC904476.2|EC904476
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|148963165|gb|EE014137.2|EE014137
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|5296121|gb|AI782996.1|AI782996
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|76921975|gb|DV168787.1|DV168787
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|6194720|gb|AW146824.1|AW146824
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|5895803|gb|AW037049.1|AW037049
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|5895869|gb|AW037115.1|AW037115
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|211510917|gb|FL028117.1|FL028117
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|148957215|gb|EC903225.2|EC903225
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCT
EST: gi|78087855|gb|DV516248.1|DV516248
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|91873431|gb|EB403388.1|EB403388
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|71325642|gb|DR799508.1|DR799508
EST:     GGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: GGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
EST: gi|6020665|gb|AW065698.1|AW065698
EST:     CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCT                         GTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT
genomic: CAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGAT

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: 205

GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 443

GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 457

GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 534

GACTCGGTGCAGTCTGGAATGTAGCTAATGTATCAAAGGGCTCAAGTGTAGCTATATTTGGTCTTGGGACCGTAGGACTTTCTgtgagtatct ... gctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaattcttacatatcaagaactgttgtaacgagacctatgtctgctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG
                         ttgtaac  putative branch site (score: 534)
        ttacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatctacataagggtccattataagttaattcttacatatcaagaactgttgtaacgagacctatgtctgctgagttagGTCGCTCAAGGTGCTAAGCTTCGAGGGGCGTCCAAGATTATAGGAGTTGATACTAATCCTGAGAAGCAAGAAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA