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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccatctgctaattgctttgaatatataattacttcaactcttacatattttatcagatataactttatatatatttaaagcgatataacttcatatgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT

Basic information

species Zea mays
transcript GRMZM2G079080_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 12
gtaagtgcca-tctgctaattgctttgaatatataattacttcaactcttacatattttatcagatataactttatatatatttaaagcgatataacttcatatgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
|| |||| |  | || ||||||| | | |   ||  || |||  | || | |||||| | | | ||                ||||   ||| |||||| |||| || |||||| || |||||||| ||||||||||| |||||||||||||||||||||||||||||||| |||||||| |||||||||||||||||| ||||||||||
gtgagtgtcggtttggtaattgcatcgca---atttttccttggaatcct-catattgtgtgaaatgc--------------ttaa---gatgtaacttaatatttgcagGTGATATAAAACGTATATGTGAAACTGACTTGGGGTTGATATCACAATGTTGCTTAACCAAACATGTTTTCAAGATCAGCAAGCAGTACCTGGCAAATGT

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA10G00530.1 (Glycine max), 3'ss of exon 4
--------------------------gtaagtgccat-----ctgctaattgctttgaatatataattacttcaactcttaca-tattttatcagatataactttatatatatttaaagcgatataacttcat---atgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
                          |||  ||  ||      || | |||| | |   | |  ||||      ||   ||   ||| || | || |  || | || ||||   |||    |||||| |  ||    | |  ||||||  |||| |||||||||||||| ||  | || || || || |||||||| || || |||||||| ||||||||||  |||||||| ||||| |||||
gtatgcccccttcaattataataaaagtacatgatatataaattggtgattgttattt-tcttcaattgtcgggacatataagctatgttctgagtttaaattctaaatattcataatttcatataattatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACGGACCTTGGTTTAATTTCTCAATGTTGTTTGACTAAGCATGTCTTTAAGATCACTAAGCAGTATTTGGCTAATGT

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 12
gtaagtgccatctgctaattgctttgaatatataattacttcaactcttacatattttatcagatataactt-tatatatatttaaagcgatataacttcat---atgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
            |  ||| ||      || |||||||  |   ||   ||   | | |  |   | ||| || || |||| | |||    ||||||||  ||    | |  ||||||  |||| |||||||||||||| ||  | || || || || |||||||| || || |||||||| ||||||||||  |||||||| ||||| |||||
------------taataaatgtacatgat-tataattgttgggacatataagcaatgttccgagtttaaattctaaatatttataatttcatataactatattttgttttcagGTGATCTCAAGCGTATTTGTGAAACCGACCTTGGTTTAATTTCTCAATGTTGTTTGACAAAGCATGTCTTTAAGATCACAAAGCAGTATTTGGCTAATGT

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S28_182V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------------------------------------gtaagtgccatctgctaattgctttgaata-tataattacttcaactcttacatattttatcagatataactttatatatatttaaagcgatataacttcatatgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
                                               | ||||  |     |||    ||    || |  ||     |  |   |      |  | |      | | |||||  |  | | |    | |||   |     ||||||||||  | ||       ||||| ||||   ||||  || | || || ||||| || |||||||||||||| ||||| |||||||||||| ||||||| ||
gtatgcatagtttctaaacttgcaagtcacacgacgaactccgtatttgagtgttaa--agtaacgatttaaggtagtggaaacgtgtggagggtgtaggctgatcttgaccttgattttatcgaactctgattttacatattgtgtggcgtgtagGTGATTTGAAGAAGCAATGTGAGACTGTACTGGGTGTGGTTTCTCAGTGTTGTTTGACCAAGCATGTTTTCAAGATGAGCAAGCAGTACCTGGCAAACGT

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S7_194V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------gtaagtgccatctgctaattgctttgaatatataattact-tcaactcttacatatttta---------tcagatataactttatatatatttaaagcgatataactt-cata-tgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
                                   ||   |  ||   ||| | ||    |  |||   || | | |||| |  |||| | |          | |  |   | ||||| ||   || |  | || ||   | |||  | |||||||||  | ||       ||||| ||||   ||||  || | ||||||||||| || || |||||||| || ||||| ||||||||||| || ||||||||
gtatgttaaggttcttgtttctatcaaacagattaaaactctttcatttaagtcctgacgacttatgggtaatgttaactttggcataatctggttggacttttatttgcgattttatttaagcttgattctatctattgtgcatggtatgtagGTGATCTGAAGAAGCAATGTGAGACTGTCCTGGGAGTGGTTTCACAATGTTGTTTGACTAAGCATGTCTTCAAGATGAGCAAGCAGTATTTAGCAAATGT

upper sequence: GRMZM2G079080_T02 (Zea mays), 3'ss of exon 12
lower sequence: PP1S173_134V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------gtaagtgccatctgctaattgctttgaatatataattacttcaactcttacatattttatcagatat--aact----ttatatatatttaaagcgatataacttcatatgtgt----agGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
               || | | | |    ||||   ||    |   || |  | ||   ||| |||| | | |  ||| |  ||      ||||  || | | || ||  ||  | |   ||||||    ||| ||  | ||       ||||| ||||   ||||| |  | || |||||||| || || || ||||| |||||||| ||||| |||||||||||||||||
gtatgttctccttcaaattacgaaccataaatttaattccccaggaaagtg-tgcaggactttcataatgtgttggattttcaatggtggttattaatgtatgaaacgtcatcgcgttgcatgtgtgtgcagGCGATCTTAAGAAACAGTGTGAGACTGTCCTGGGGGTCGTGTCTCAATGTTGTTTGACGAAACATGTATTTAAGATGAGCAAACAGTACTTGGCAAATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatcagatataactttatatatatttaaagcgatataacttcatatgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT
                                   atataac  putative branch site (score: 3)
         atataactttatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgccatctgctaattgctttgaatatataattacttcaactcttacatattttatcagatataactttatatatatttaaagcgatataacttcatatgtgtagGTGACATCAAACGTATTTGTGAAACTGATTTGGGGTTGATATCACAATGTTGCTTAACCAAGCATGTTTTTAAGATCAGCAAGCAGTACTTGGCAAATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG