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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatgactgtttccccttgtattgtctcagttcatctaattgtatgactgccctaaaatgaagttactcatttcttgctgttgaaccag

Basic information

species Zea mays
transcript GRMZM2G169095_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g33330.1 (Oryza sativa), 5'ss of exon 15
GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcg--aatgactgtttccccttgtattgtctcagt---tcatctaattgtatgactgccctaaaatgaagttactcat----ttcttgctgttgaaccag
||||||||||||||  ||||| ||||||| ||||||   ||||| |||||||||||||| ||||||||||||||||| |||||||||||||| |||||||||  |  | | |||| |||  | | |  | |  ||||   | |||| ||||||   || || |  ||     | |  |||    ||  |||| || | | ||
GCTCTTGATATTCTCGCACGAACACCACTTTGGAGAAGCGGTCTGGACTATCGGCATGGCACAGGCCATGGAATTGGGTCTTATTTGAATGTTCATGAAGgtcagatagttactggttcatcctcttctatgacagtaaattatctgattgtagttctacctttgaaatgtttaatccatattgtttgtgctcttaatctag

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os06g45360.1 (Oryza sativa), 5'ss of exon 13
GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcga------atgactgtttccccttgtattgtctcagt---tcatctaattgtatgactgccctaaaatg---aagttactcatttcttgctgttgaaccag
||| ||||||||||  ||||| ||||||| ||||||   |||||||| || ||||| |||||||||||||| |||||||||||||||||||| |||||||||  ||      ||  ||| |||  | | |  | |  ||||   | |||| ||||||   || || | |||||   ||   | ||  ||  ||||    | ||||
GCTATTGATATTCTCGCACGAACACCACTTTGGAGAAGTGGTCTTGATTACCGGCACGGTACAGGCCATGGTATTGGATCTTATTTGAATGTTCATGAAGgtcagatactcaattgctggttcatcctcttctatgacagtaaattatctgattgtagtgctaccttgaaatgtttaatccattctgtttgtgcttacaacccag

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os11g33340.1 (Oryza sativa), 5'ss of exon 14
GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcga-atgactgtttccccttgtattgtctcagttcatctaattgtatgactgccctaaaa--tgaagttactcatttcttgctgttgaaccag
||||||||||||||  ||||  ||||||| |||| |   |||||||| |||||||| || |||||||||||  ||||||||||||||| ||| |||||||||  || |    |   | | |||  || |    |  | |||  ||| ||||  | |  ||||   | || |||  |  ||  |||| || | ||||
GCTCTTGATATTCTCGCACGGACACCACTTTGGAAAAGTGGTCTTGATTATCGGCACGGCACAGGCCATGGGGTTGGATCTTATTTGACTGTTCATGAAGgtcagatactggttcattctcttcgatggcagtaaataatcggattatatgggtactttaaatgtttaatttatactgtttgtgcttttaatccag

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|50323429|gb|CO518555.1|CO518555
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|60395851|gb|DN228721.1|DN228721
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|211089695|gb|FL030414.1|FL030414
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|211089690|gb|FL030409.1|FL030409
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|148948655|gb|EC898569.2|EC898569
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|71439289|gb|DR820339.1|DR820339
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|71760087|gb|DR958024.1|DR958024
EST:     TGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|67010801|gb|CO439550.1|CO439550
EST:     TCGGCATGGTACAGGCCATGGAATCGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|211089693|gb|FL030412.1|FL030412
EST:     TATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTTCAAG
genomic: TATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|211089692|gb|FL030411.1|FL030411
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|86467956|gb|DY234326.1|DY234326
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|211089696|gb|FL030415.1|FL030415
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|67018778|gb|CO447527.1|CO447527
EST:     CGGCATGGTACAGGCCATGGAATCGGATCTTATTTGAATGTCCATTGAAG                         -TCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGNCA
genomic: CGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCAT-GAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTG-CA
EST: gi|211089691|gb|FL030410.1|FL030410
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|211089694|gb|FL030413.1|FL030413
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
EST: gi|211092150|gb|FL030416.1|FL030416
EST:     TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAG                         GTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG
genomic: TCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAG

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: 227

GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 238

GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 255

GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatga ... gttgaaccagGTCCTCATCTAATTAGCTTCAGACCTTCTGCTCGAAATGTACCGCTGCAAGCATCAATGACTGTGACAGATG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCTTGATATTCTTTCACGAGCACCACTCTGGAGAGAGGGTCTTGACTATCGGCATGGTACAGGCCATGGAATTGGATCTTATTTGAATGTCCATGAAGgttcgaatgactgtttccccttgtattgtctcagttcatctaattgtatgactgccctaaaatgaagttactcatttcttgctgttgaaccag

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