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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatgagttttttgttctacagctatgccctatgctaaattcactaacaacatgagacacttctaatcgtctcttgttcctggtataccttatgtaaatgctatctgttttaaagttttctccctgcactgtcttgtaaaagtgtatgttgagcctgtttgctagtaaaattataatatttcag

Basic information

species Zea mays
transcript GRMZM2G315931_T02
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G315931_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os08g37950.1 (Oryza sativa), 5'ss of exon 13
GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatgagttttttgttctacagctatgccc--tatgctaaattcac----taacaacatgagacacttctaatcgtctcttgttcctggtataccttatgta--aatgctatctgttttaaagttttctccctgcactgtcttgta---aaagtgtatgttgagcctgtttgctagtaaaattataatatttcag
||||| ||||||||||||||||||||||| || |||||||||||||| |||||||| ||||| |||||||| ||||||||| | |||||||| || ||||||| |||| || ||| || | ||| | ||     |||||    | |      ||  ||  | | | ||||| | |  |||  | |||  | |||   ||||||   ||  |||    |||   |||| |  |  | |    |  ||||   ||  ||     ||||    | ||||    |  | ||  | ||||||
GCAAAAGATGGATCCTTCATGGAAGAACCTGGGTCTGGTGCTGTGGCGACCATTGGCGAGAAACAGGTTTCAGTTGGAACACTTGATTGGATCAGGAGgtacaaatgaattatttattgtgcagttgtgatgaatatgccttgtccttctgatagaaaatttacaaacttc-agttctctactcttcacgctatctgttatgtcttaagtctactattttcttagttctagcaatacttaatgatgtactaaatatgatcactgagggactctgctcactacctaat--tgtttcag

upper sequence: GRMZM2G315931_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA08G07710.1 (Glycine max), 5'ss of exon 13
GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatgagttttttgttctacagctatgccctatgctaaattcactaacaacatgagacacttctaatcgtctcttgttcctggtataccttatgtaaatgctatctgttttaaagttttctccctgcactgtcttgtaaaagtgtatgttgagcctgtttgctagtaaaattataatatttcag
| ||| |||||| | ||| |||||||||| ||||||||||||||||| || |||  ||| ||  ||||||||||||| |||||||| |||||||  |||||| |   |||||     || |  | ||  |  |||  ||  |||   ||             || | |   | | |  ||      ||   ||||  | | | ||| |  || |||                                                                      
GTAAAAGATGGAACATTCCTGGAAGAACCTGGATCTGGTGCTGTGGCAACAATTTATGACAAAAAGGTTTCTGTTGGGACATTAGAATGGATTACCAGgtactt---agttt----gtccaaggatacacaatatagtatgttcctcaat---------ttttttttaatatttttcatta-----atttattataaagaggatatttccttcaaacaa-------------------------------------------------------------------

upper sequence: GRMZM2G315931_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA05G24520.1 (Glycine max), 5'ss of exon 10
GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatgagttttttgttctacagctatgccctatgctaaattcactaacaacatgagacacttctaatcg-tctcttgttcctggtataccttatgtaaatgctatctgttttaaagttttctccctgcactgtcttgtaaaagtgtatgttgagcctgtttgctagtaaaattataatatttcag
| ||| |||||| | ||| |||||||||| ||||||||||||||||| || |||| | | ||  ||||||||||||| || || || |||||||  |||||| |    ||| ||||  | |  | ||  |  |||  ||  |||   || ||  | | | | |||| ||   | | || |     | |||  |  |  |||                                                                                      
GTAAAAGATGGAACATTCCTGGAAGAACCTGGATCTGGTGCTGTGGCAACAATTGATAACAAAAAGGTTTCTGTTGGGACGTTGGAATGGATTACCAGgtactt---ggttatttgc-ccaaggatacacaatatagtatgttcctcaaaaattttaaatatttcttattaatttattataaacaggatatttccttcaaac-------------------------------------------------------------------------------------

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|32929758|gb|CF034570.1|CF034570
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
EST: gi|78104271|gb|DV522689.1|DV522689
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
EST: gi|211170367|gb|FL103276.1|FL103276
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
EST: gi|32823148|gb|CD962870.1|CD962870
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGACCATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
EST: gi|13125965|gb|BG316640.1|BG316640
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
EST: gi|32929848|gb|CF034660.1|CF034660
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGACCATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
EST: gi|32929738|gb|CF034550.1|CF034550
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
EST: gi|32929733|gb|CF034545.1|CF034545
EST:     ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAG                         GCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC
genomic: ACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTC

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), 49 (downstream exon)
Score: 142

GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTCTGTTGCATATGTAGCAGTGAATGGTGCTCTGGCTGGTCTTATTTGTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 200

GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTCTGTTGCATATGTAGCAGTGAATGGTGCTCTGGCTGGTCTTATTTGTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 112

GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTCTGTTGCATATGTAGCAGTGAATGGTGCTCTGGCTGGTCTTATTTGTTTT


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 165

GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatga ... aatatttcagGCATGGGGTCATTCACAACCCCTTCCCAGAAGCAGAGCATTTTGGCCAGTCTGTTGCATATGTAGCAGTGAATGGTGCTCTGGCTGGTCTTATTTGTTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAATGATGGATCCTTCATGGAAGAACCAGGATCTGGTGCTGTGGCTACCATTGGTGAGAAGCAGGTTTCTGTTGGAACATTAGATTGGATTAGAAGgtacatatgagttttttgttctacagctatgccctatgctaaattcactaacaacatgagacacttctaatcgtctcttgttcctggtataccttatgtaaatgctatctgttttaaagttttctccctgcactgtcttgtaaaagtgtatgttgagcctgtttgctagtaaaattataatatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC