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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcattgccttgattaccattgacttctcttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA

Basic information

species Zea mays
transcript GRMZM2G016930_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
aaacatctagagtgctcatctgttg-agctgtgaaatactattttggttgtgc-attgccttgatt-accattgacttctcttcaactgaatctact-tcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
     |    ||||    |||| || ||      | || | || |  ||| || |||| ||| ||| |||| | ||| || |      | |||| || | |||||| || |||||||| |||||||| || || || |||||||||||||| |||||||| ||||| ||||| ||||| ||||| |||||||| || ||  |||
----tttctcagtgaatctctgctgtagtgaactattattgttattattgagcgattgtctttatttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G02180.1 (Glycine max), 3'ss of exon 2
aaacatctagagtgctcatctg-ttgagctgtgaaatactattttggttgtgcattgccttgattaccattgacttctcttcaa-ctgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
  |  | | | |   |    ||  | | | ||   |  | |||||  |       ||  |    |   ||    | ||  | ||  |        |  | |||| ||||||||||| || || ||||| || || || ||||| || || |||||||| ||||| ||||||||||| || || || |||||||||||  |||
--atgtattgggcatttgcttggctcatcagtcttaatccattttaatgaattggtgaatctggttttatgttttccttctaaaattttgggctttgtatagGTTGTAGAGGATGGATACGAGTTTTTTGCCAAGCGTCAGCTAGTGACTATATTCTCCGCACCAAACTACTGTGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G37370.1 (Glycine max), 3'ss of exon 2
-aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcattgccttgattaccattgacttctcttcaact--gaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
 |  |   |  | ||  ||| || |  |||    | |  || |    | ||  ||   || | |||   ||  | | |    |  |  |  | |   |  ||||| ||||||||||| ||||| ||||| || || || ||||| || || |||||||| ||||| || ||||| || || || || |||||||||||  |||
tatgctgatgtattgggcatttgcttggctcatcagtcttaatccattggtaaat---ctggtttaatgttttccttttaaaattttgggctttgtgtttcagGTTGTAGAGGATGGATATGAGTTTTTTGCCAAGCGTCAGCTGGTGACGATATTCTCCGCACCAAATTACTGCGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: AT4G11240.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------------------------aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcat-----------tgccttgattacca--ttgacttctcttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
                                                                     ||    |    ||     | | |  |||||  ||  |  |||||  ||           |   ||  | ||||     | || |  | ||||  |         ||||| ||||| ||||| || || || || |||||  | || || || ||||||||||| ||||| || |||||||| ||||| ||||||||||||||| |||
gtaaagctaaaatttattccttgagttctctcttttgatttctctggattggtttgttcttctctgtgactgttctctgaattcagagggttaagaaatcataactcagttgttaatgcaaggatctgtagttttttcaccaagccaagttttacttaactatactgttcctgcagGTTGTAGAAGATGGATACGAGTTCTTTGCAAAGAGACAACTAGTGACAATATTCTCTGCACCCAATTACTGTGGCGAGTTTGACAATGCTGGTGCATTGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv02s0025g00480.t01 (Vitis vinifera), 3'ss of exon 2
aaacatcta-gagtgctcatctgttg-agctgtgaaatactattttggttgtgcattgccttgattaccattgacttctcttcaactgaatctac-ttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
  |||||   | ||| | ||    ||  | | ||  ||  | ||||||||| |  |    || |||   | |    | | |     ||    |   ||  ||||| || || ||||| ||||| ||||| |||||  | ||||| || || |||||||| ||||| || |||||||| ||||||||||||||||||||  |||
--acatccctgtgtgtttattatctgtggttatgtgat-tttttttggttgagactcaaattaattgtgacttgtgtttttgatcttgggcatgtatttccagGTTGTGGAAGATGGGTATGAGTTTTTTGCAAAGAGGCAGCTAGTGACCATATTCTCGGCACCAAATTACTGTGGCGAGTTCGACAATGCTGGTGCCATGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: EDO97337 (Chlamydomonas reinhardtii), 3'ss of exon 4
----------------------------------------------------------------aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcattgccttgattaccattga-cttctcttcaactgaatctact-tcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
                                                                |   |    | || | |  ||   | | | |    |  |    |   ||  |   |    ||   ||  ||| |||  |||    || || |  | |   |||| || ||||| || || || || |||||||| ||||||||||| || |||||||| || ||||||||||| || |||||||| ||||| || ||  |||
gtgcgggtcgtcgcctaggtgttccgcgggtttatggggttggcggaacacgcatcgcatgtcaagggacggggggtacccgactccgggggtcttgtgtggtcccgtatctgcccgaagtgcagagctcctctgaactttgcttgtcttgcatgtggtattgtagGTGGTGGAGGAGGGGTACGAGTTCTTCGCAAAGCGCCAGCTTGTGACCATATTCTCGGCGCCGAACTACTGCGGCGAGTTCGAGAATGCGGGAGCGATGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcattgccttgattaccattgacttct--cttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
 |     ||   | ||  | |  |  | |  |  ||  ||  | | |    | |    | ||   |   | | |  |  |||     | ||        ||||| || ||||||||||||||||| ||||| || |||||||| || || || ||||| |||||||| |||||||| || || || ||||| |||||  |||
-attgattaatttacttttttcgttgggta-gggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S97_286V6.1 (Physcomitrella patens), 3'ss of exon 3
-aaacatctagagtgctcatctg-ttgagctgtgaaat--actattttggttgtgcattgccttgattaccattgacttctcttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
 |   || |  |   |  ||  | ||||  |||    |  || |   |  || |  ||| | |||  ||| ||   ||  |||      ||   ||| | |||||| |||||||||||||||||||||||||| || ||||| || || || || || || || || || || ||||| || || || ||||| |||||| |||
gacgaatttgaacctccgatgcgattgacatgtctcttccaccaccatacttttatatt-ctttgtatactat--gctgatctgtgtgggatgttacat-acagGTAGTAGAGGATGGTTATGAATTTTTCGCTAAGCGCCAACTGGTTACCATTTTTTCTGCTCCAAATTATTGTGGTGAATTTGATAATGCGGGTGCAATGA

upper sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S22_185V6.1 (Physcomitrella patens), 3'ss of exon 3
---------aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcattgccttgattaccattgacttctcttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
         ||   |  |  ||| |    | |     || | |  | ||  ||  |  ||   ||  |  | |||   |||| | | |      |||| |      ||||| || |||||||||||||| ||||| || ||||||||||| || || || ||||| ||||| || |||||||| || || || ||||| |||||  |||
gattttacaaattgtacaatgtgattcagtctcctaatgggtagaattaccttattcctggtgtgtttcaagtac---tgacatgtgt------gaatgtcacatgcagGTAGTGGAGGATGGTTATGAGTTTTTTGCTAAACGCCAGCTGGTCACTATTTTCTCTGCACCAAATTACTGTGGTGAATTTGATAATGCGGGTGCGATGA

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|22714197|gb|BU197459.1|BU197459
EST:     CCGAGTTTCTTCAGAAACATGATCTAGATTTGATCTGCAGGGCCCACCAG                         GTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA
genomic: CCGAGTTTCTTCAGAAACATGATCTAGATTTGATCTGCAGGGCCCACCAGgtattcatta ... tacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA
EST: gi|211276254|gb|FL232543.1|FL232543
EST:     CCGAGTTTCTTCAGAAACATGATCTAGATTTGATCTGCAGGGCCCACCAG                         GTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA
genomic: CCGAGTTTCTTCAGAAACATGATCTAGATTTGATCTGCAGGGCCCACCAGgtattcatta ... tacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA
EST: gi|32911548|gb|CF016360.1|CF016360
EST:     GGGCCCACCAG                         GTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA
genomic: GGGCCCACCAGgtattcatta ... tacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA
EST: gi|71329876|gb|DR801655.1|DR801655
EST:     CCGAGTTTCTTCAGAAACATGATCTAGATTTGATCTGCAGGGCCCACCAG                         GTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA
genomic: CCGAGTTTCTTCAGAAACATGATCTAGATTTGATCTGCAGGGCCCACCAGgtattcatta ... tacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtgcattgccttgattaccattgacttctcttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA
                     cattgac  putative branch site (score: 3)
                                           tctacttc  putative PPT
             ttgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcattgccttgattaccattgacttctcttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG