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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtaatcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

Basic information

species Zea mays
transcript GRMZM2G126453_T01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 21
--gtaatcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgc--aattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
   || | |  ||    | |||| ||| |  ||         |||||||  |  ||    ||||      | | || |||||| |   |||   ||  ||||||||||||||||| |||||||| || ||||||||||| ||||| ||||| |||||||| || |||||||||||||||||||| ||||| ||||| || ||||
ctatattttgggacggatggagtattatatgttggctacctaattttctctattta----agtcctatcttaaaaattgcctctggtaaatctgttacttgcagCCTTGCAAGGGAATATTGCTGTTTGGACCTCCTGGTACTGGGAAAACCATGCTTGCTAAGGCAGTAGCAACTGAAGCAGGTGCTAACTTCATTAACATAT

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 17
gt-aatcttagatatgtcgagttttaaaacttcatctgta-gattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
|| ||   |    || |    | || |||   | | || | ||  || ||||     |   | || |    ||  ||    |    | | | ||   |  |||||||||| || ||||||||||| || ||||||||||| |||||||| |||||||| || || |||||||||||||| || || ||||| || || || |
gtgaaagattttcattttagttgtttaaatgacttgtgaaagaaattgttgagtagatcatgccatgtgtgtagcacctaattgtaattactttgggtatagCCTTGCAAAGGAATATTGCTTTTTGGCCCTCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 20
----gtaatcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcatt--ctttg----cagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
    |||   ||   | |     | ||||||     |   | | |  || || |     |    |  | ||| | |   |  | || || |  | |  |||||     ||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| || || |||||||||||||| || || |||||||| || || |
gttggtagattttctttttagttgctttaaatgacaagtggaacacattttttagtagatgatattcatatcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 17
---gtaatcttagatatgtcgagttttaaaacttcatctgta-gattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
     ||   |    || |    | || |||   | | || | ||  || || |     |   | || |    ||  ||    |    | | | ||   |  ||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| || || || ||||||||||| || || ||||| || || || |
gtgaaaaatattttcattttagttgtttaaatgacttgtgaaagacattgttaagtagatcatgccatgcgtgtagcacctaattgtaattactttgggtatagCCTTGCAAGGGAATATTGCTTTTTGGCCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTGGCAACTGAAGCTGGAGCAAATTTTATTAACATTT

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 16
----gta-atcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcatt--ctttg----cagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
     || || ||   | |      ||| ||    |  |        ||| ||     |  ||| || | ||| | |   |  | || || |  | |  |||||     ||||||||||||| ||||||||||| || || |||||||| |||||||| |||||||| || || |||||||||||||| || || |||||||| || || |
gttgatagattttctttttagttgctttaaatgacttgtggaacacattttttagtagatcatattcga-atcatgtgtgtagcacctcattgtaattactttggatatagCCTTGCAAGGGAATATTGCTTTTTGGGCCCCCTGGCACAGGAAAAACAATGCTTGCAAAGGCTGTAGCAACTGAAGCTGGAGCAAATTTCATTAACATTT

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaatcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
|||   ||   |       | | ||    || || |||   || | |   ||||| |||    | | |  | |  |   |  |   || | |    |||||||   || || ||| || | || ||||||||||| |||||||| || ||||| || ||||||||||||||||| || ||||| |||||||||||||| |
gtaccttttatt-------gctatacggatttatttgttagttgt-tactcctac-ataactgaaaccaaaca--tatatttgatgtttaat----gcagCCTACGAAAGGTATACTGTTGTTTGGACCTCCTGGTACTGGAAAGACGATGCTGGCAAAAGCAGTAGCAACTGAGGCTGGCGCAAATTTCATCAATATCT

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: AT4G24860.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaatcttagatatgtcgagttttaaaacttcatctgtagattttc----ttgacctactatagtcaagatcttataactg--cctccgcaattcattctt-tgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
   || |    |   || |    |||  ||||     || | |||     || || |  |  | |   |   |  |||     || |     ||| |  || |||||||||| || || ||  |  | || ||||||||||| |||||||| || |||||||| |||||||| ||||  ||||| |  || || |||||||| || |
---atttggctttcctcaa----taattcttctctcctaaaatttggtagttaacgttatgcattggtggcttcttaatcagtccgctcttgttcgtctttatgcagCCTTGTAAAGGAATTCTTTTATTTGGACCTCCTGGAACTGGAAAGACCATGCTTGCAAAAGCAGTGGCAAAGGAAGCTGATGCGAACTTCATCAACATCT

upper sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 20
--------------------------------------------gta-atcttagatat---gtcgagtttta----aaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
                                             || || ||   |||   || || ||||      || |      |||  |||| |  |  |  |    |  |  |||   | |||  |  |   ||  |  ||| |||||||||||||| ||  | || || || |||||||| ||||||||||| |||||||| || || || |||||||| ||||| || ||||| ||||| ||||
gttaggtgtttcacatgttttatttctttattgtgtatgtatatatatatattgtgtatctggtggaattttcttttgaattatggaagtaagttttatctaattcatgccttgtatgtctatcatctgaat--gaggttactatttttcagCCTTGCAAGGGAATTCTTCTATTTGGGCCTCCTGGGACTGGAAAAACAATGCTTGCGAAGGCGGTTGCAACTGAGGCAGGTGCAAATTTTATCAACATAT

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|58029637|gb|CX725064.1|CX725064
EST:     TGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAG                         CCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATG
genomic: TGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATG
EST: gi|32934898|gb|CF039710.1|CF039710
EST:     TGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAG                         CCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATG
genomic: TGCTCCCTTTGCAAAGACCTGAGTTGTTCTGCAAAGGGCAGTTAACAAAGgtagcatcat ... ttctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT
                       ttataac  putative branch site (score: 2)
                                         ttcattcttt  putative PPT
                    atcttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttagatatgtcgagttttaaaacttcatctgtagattttcttgacctactatagtcaagatcttataactgcctccgcaattcattctttgcagCCTTGCAAGGGGATATTGCTTTTCGGACCTCCTGGCACTGGAAAAACTATGCTTGCCAAAGCAGTAGCAACTGAAGCAGGCGCTAATTTCATCAATATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC