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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcactaattgtttgattgctttcttctacatgagtatagaagagtgtctgactatattcagtgtgcactcatgctcaatattattgttatatgatc...

Basic information

species Zea mays
transcript GRMZM2G169095_T02
intron # 4
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 15
lower sequence: LOC_Os11g33340.1 (Oryza sativa), 5'ss of exon 16
CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcactaattgtttgattgctttcttct--acatgagtatagaagagtgtctgactatattcagtgtgcactcatgctcaatattattgttatatgatc
|||||||||||| ||||||||||| || ||     |||| |||||| |||| ||||||||||||||||| ||||||||||||||||||||||||||||||||||||| | ||||||  ||  ||   || |  ||       | |   | |||    || | |      | || |  ||  | ||||  |||| |   ||  
CTTTGGTATAAGGTTGGAGAATGTTCTGATAGTTCAAGATGCCAATACTAAATTTAATTTTGGAGATAAGGGTTATTTGGCATTTGAACATATAACATGGgtaagcattgattgttcaatctctaaattattaactctcactttggtaactgttcttctctttgtttcattcattt-tggactatatc-ttgtaaccagaag

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os06g45360.1 (Oryza sativa), 5'ss of exon 15
CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcactaattgtttg-attgctttcttctacatgagtatagaagagtgtctgactatattcagtgtgcactcatgctcaatattattgttatatgatc-
|||||||||||| ||||||||||| || ||    ||||| |||||| |||| ||||||||||||||||| ||||||||||| |||||||||||||||||||||||         | |  |||   ||    ||      |        ||      | |   || || | || |    |   ||||    |||  || ||  
CTTTGGTATAAGGTTGGAGAATGTTCTGATAGTTAAAGAAGCCAATACTAAATTTAATTTTGGAGATAAGGGTTATTTGGCTTTTGAACATATAACATGGgtaagtttcttcaatctccattttattaaattattaactttctctttggtaatctccaagtctccgtat-caatttcacaagatatcccggttg-ataatac

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 15
lower sequence: LOC_Os11g33330.1 (Oryza sativa), 5'ss of exon 17
CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcactaattgtttgattgctttcttctacatgagtatagaagagtgtctgactatattcagtgtgcactcatgct-caatattattgttatatgatc---
|||||||||||||||||||||||| || ||    ||||| || ||| |||| | |||||| |||||||| ||||||||||||||||||||||||||||||||||| | |  || ||  ||  |  | || |   | | |    ||   | | ||   |  |  |||||     || | | || ||||      |||   ||   
CTTTGGTATAAGATTGGAGAATGTTCTGATAGTTAAAGAGGCTAATACTAAATATAATTTCGGAGATAAGGGTTATTTGGCATTTGAACATATAACATGGgtaagtattgtttcttcaatctccattttat---taaattgttaactctctttggtaac-tgtagtgtttctccaagtttcagtatttcgtaaatacagtcttc

upper sequence: GRMZM2G169095_T01 (Zea mays), 5'ss of exon 15
lower sequence: Vv04s0023g01300.t01 (Vitis vinifera), 5'ss of exon 15
CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcactaattgt-ttgat--tgctttcttctacatgagtata-gaagagtgtctgactatattcagtgtgcactcatgctcaatattattgttatatgatc
|||||| ||||||||||||||||| ||  |   ||| || ||  || | || || |||||||| ||||| ||||| |||||||||||||| ||||||||||||||      || | || ||  |    | || |   |   | |  | |  || ||||  | | ||   | |   ||  |      |    ||  | | | || 
CTTTGGCATAAGATTGGAGAATGTCCTCGTAATCAAGGAGGCTGATACAAAATTCAATTTTGGTGATAAGGGTTACTTGGCATTTGAACACATAACATGGgtaagtttattttatattaatgatatccttttttgttttcttgtgcgcaatgtatctggttttttt---tttttccttgtagcaggttccttttattttttat-

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|6851547|gb|AW352557.1|AW352557
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCGTACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|28984456|gb|BQ539072.2|BQ539072
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|60395851|gb|DN228721.1|DN228721
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCGTACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|148948655|gb|EC898569.2|EC898569
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|71760087|gb|DR958024.1|DR958024
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211089692|gb|FL030411.1|FL030411
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATA
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATA
EST: gi|211507045|gb|FL413323.1|FL413323
EST:     ATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: ATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211092150|gb|FL030416.1|FL030416
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|67010801|gb|CO439550.1|CO439550
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCGTACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211089693|gb|FL030412.1|FL030412
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|86467956|gb|DY234326.1|DY234326
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|211089696|gb|FL030415.1|FL030415
EST:     GTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAAWCATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGA
genomic: GTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAA-CATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGA
EST: gi|211089695|gb|FL030414.1|FL030414
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCC-TGTT
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTT
EST: gi|211089690|gb|FL030409.1|FL030409
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTG
EST: gi|166621297|gb|EG158029.1|EG158029
EST:     GGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGAGCTTCTGACCCCTGTTGAG
genomic: GGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
EST: gi|71439289|gb|DR820339.1|DR820339
EST:     AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGG                         GCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG
genomic: AGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcacta ... taatgtgtagGCTCCATACCAGACCAAGCTGATAGACACCGGGCTTCTGACCCCTGTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTTGGTATAAGATTGGAGAATGTACTTATTTGCAAAGACGCCAATGCTAAGTTTAATTTTGGAGATAAAGGTTATTTGGCATTTGAACATATAACATGGgtaagcactaattgtttgattgctttcttctacatgagtatagaagagtgtctgactatattcagtgtgcactcatgctcaatattattgttatatgatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT