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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttctgcatagcgattatgtcttattttgttgattttggcaaaactaagctctcttattgtctgcagtacaaacctattttaacatttgttataataaagcattattatggttactaaaatatatttactatgataactaactagtggtgctggtccag

Basic information

species Zea mays
transcript GRMZM2G351582_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G351582_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os08g36774.1 (Oryza sativa), 5'ss of exon 4
GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttctgcatagcgattatgtcttattttgttgattttggcaaaactaagctctcttattgtctgcagtacaaacctattttaacatttgttataataaagcattattatggttactaaaatatatttactatgataactaactagtggtgctggtccag
|||||| ||| |||||||||||||||| ||||| || |||||||| || ||| | |||||||| |||   |||||||  |||||||| ||||||      |  | | | |||| ||||      |      | || |   | ||    ||    |   ||||    ||||     ||| ||     |  | |                                                       
GAACAATGAGGTTCAGTTTGCTGGACAGCTCCAGCCGAAGGGATGTTGTTACCGTTTGGAGGTCCCGCGCGGGCAGAACGAGgtatg-gttctgtggcatggctgt-ttttatgttgtcaccaattt----attaggtggtgtttggatccagggactaaac----tttagtccctgtcatgtcggatgaat-------------------------------------------------------
















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|20507104|gb|BQ279486.1|BQ279486
EST:     CCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: CCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|149027382|gb|EE046514.2|EE046514
EST:     AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|149058050|gb|EE156735.2|EE156735
EST:     AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|87152120|gb|DY396909.1|DY396909
EST:     AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|211353775|gb|FL303049.1|FL303049
EST:     ACCCAAGGGATGCTGCTACAGCTTGGAAGTTCCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: ACCCAAGGGATGCTGCTACAGCTTGGAGGTTCC-GTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|18450704|gb|BM428982.1|BM428982
EST:     AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|78022867|gb|DV491254.1|DV491254
EST:     AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|26456768|gb|CA828351.1|CA828351
EST:     AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
EST: gi|148996196|gb|EE035468.2|EE035468
EST:     AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAG                         ATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG
genomic: AACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG

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: 44 (upstream exon), 46 (downstream exon)
Score: 351

GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 271

GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 295

GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 215

GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttc ... gctggtccagATGCTGAATCGTCAGGTCGTGAAGTCTGATTCAGCGACTATCAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAACGAGATTCAGTTTGCTGGACAACTCCAACCCAAGGGATGCTGCTACAGCTTGGAGGTTCCGTTGGGGCAGAGTGAGgtatgtgttctgcatagcgattatgtcttattttgttgattttggcaaaactaagctctcttattgtctgcagtacaaacctattttaacatttgttataataaagcattattatggttactaaaatatatttactatgataactaactagtggtgctggtccag

- - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG