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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaataacattttctttcatgttgtgtgttgtcttcccatcctctcttgttattcaacttatactgatgacaggcattgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC

Basic information

species Zea mays
transcript GRMZM2G109039_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G109039_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g48964.1 (Oryza sativa), 3'ss of exon 5
gtacaataacattttctttcatgttgtgtg-----ttgtcttcccatcctctcttgttattcaacttatactgatgacaggcattgtt----gtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC
|||   || | | || ||   ||||   |      || | | | |  | |||    ||  |  | |  || |||||       || ||     ||||||||||  | ||||||||| | ||||| |||| |  ||| ||||||||||||||| |||||||||||||||| ||||||||||||||||||||||||||||
gtatggtaccttctttttctttgttccatcaatttttatttactctgcttctaagttttatgtattagtattgatgtttcatgtttttcttattacagAAGCACCCTGGAAGTTTACTTGAGGGTTTTTCTGGGACCCAAGTTAGTACCTTGTCAGTCAAGGACAATTTGCTGGTAGCTGGTGGGTTTCAAGGAGAGC
















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|58029875|gb|CX725302.1|CX725302
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|60347828|gb|DN214801.1|DN214801
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|8368895|gb|BE051840.1|BE051840
EST:     AAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: AAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|20301188|gb|BQ164131.1|BQ164131
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|453303|gb|T15277.1|T15277
EST:     GTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|67012835|gb|CO441584.1|CO441584
EST:     TGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTAC
genomic: TGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAA-GGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTAC
EST: gi|20301181|gb|BQ164124.1|BQ164124
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|20300911|gb|BQ163854.1|BQ163854
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|20301275|gb|BQ164218.1|BQ164218
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCATGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|20300918|gb|BQ163861.1|BQ163861
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
EST: gi|26456084|gb|CA827667.1|CA827667
EST:     GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAG                         AAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC
genomic: GTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACC

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: 519

CATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 789

CATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 892

CATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 631

CATCTACCTAGTATCTCATTACTCAATTCGTCACTGGTCAGCATTGAGTGGTGTGGATACTGAACTTATCAACGTCCAAGGACATGTGGCACCAAGGGAGgtacaataac ... tgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcccatcctctcttgttattcaacttatactgatgacaggcattgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC
                             tactgat  putative branch site (score: 631)
                 ttattcaacttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaataacattttctttcatgttgtgtgttgtcttcccatcctctcttgttattcaacttatactgatgacaggcattgttgtacagAAGCATGCAGGAAGTTTATTAGAGGGGTTTTATCAGACTCAAGTTAGTACCTTGACAGTCAAGGACAATTTACTGGTAGCTGGTGGGTTTCAAGGAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA