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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG

Basic information

species Zea mays
transcript GRMZM2G158162_T01
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os07g48200.1 (Oryza sativa), 3'ss of exon 4
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttag--taacttatacatca---aggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttctttta-tcttccttgactatattt---tgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
              || ||| ||   ||  |  | | |||||| |||||| |||   |  |   |  ||   ||  ||    || |   |  ||||  ||  | ||| |  |    ||   || | ||||  ||||||  | | |       | ||| | | |  | ||||  | |||||| |||||||||   | |||||||||||||||| || || ||  |||| |||||||| || || || |||||||||||||||||||||||||||||||| |||||||| ||||| |||
--------------gtatcctta---ttatatttatcaacttcttggtgatattatgcataagtagctaacatactttgcgtataatacaatctctgtaactgatcaatcagggcgaattatt-tcatattgtgcatacctattt-------ctgatctggatgctattttggttttccttaactatatttctcttcaagTTCAAATTCCACCATTGTCCCCCTGTTTGAGAAGGTTCTAAGCGCCAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTACCAAAAGCCTGTGCGGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA14G38490.1 (Glycine max), 3'ss of exon 1
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                                                                    ||| ||| ||   |  ||| |  ||  |  ||       || | ||  | || |  ||  ||     | | ||||||   |||  |   ||||  || || || || || |||||||| ||||||||  ||||||| ||||||||||| || || || || |||||||| |||||| ||||||| |||
---------------------------------------------------------------------------------------------------gcat-aggttttgcctgttaca-catcgtctatg------ttatata-taaatttgattcatcaccagtttcccttgatgttatcattacagtttgaagtctactatagTGCCATTGTTTGAGAAGGTATTGAGTGCCAGTGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGTGCTGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA02G40280.1 (Glycine max), 3'ss of exon 3
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                                                          || ||||    | |||  ||   |  ||||   |   |  | |   | |||  |  | | || |  ||  ||  |  | | ||||||   |||  |   ||||  || || || || || |||||||||||||||||  ||||||| || |||||||| || || || || |||||||| |||||| |||| || |||
-----------------------------------------------------------------------------------------ttataatataggagtagatttggcctgttatt-caccgtctacattatactt-cgatataaatttgattcatcactagtttcccttgatgttatcatcacagTTTGAAGTCTACTATAGTGCCATTGTTCGAGAAGGTATTGAGTGCCAGCGATGCAGGTCGAATTGGTCGACTTGTTCTCCCAAAATCTTGCGCTGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA18G05840.1 (Glycine max), 3'ss of exon 6
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                                                       |  |   ||   | ||| || |      |||  || || ||  |  |   |||  |   | | |  | |||| |    ||  |||| | | | |||  |   ||||  || |||||  | || ||||| || ||||||||  ||||||| ||||||||||| || || || || |||||||| |||||||| ||||| |||
-----------------------------------------------------------------------------------gtatcctttatattttttatttggttg----tcttg-aacat-atataatagactctgatagtataaagttggtttattcagtagtttcccttaatgtatgat---agTTTGAAATCCACTGTAGTGCCATTATTTGAGAAGGTGTTGAGTGCCAGTGATGCAGGTCGAATTGGCCGTCTTGTTCTCCCAAAAGCCTGTGCTGAG

upper sequence: GRMZM2G158162_T03 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g08100.t01 (Vitis vinifera), 3'ss of exon 4
gtatccttgataaggtctccatacatttgaaactgtgaacttcctggtgacattgatctcagacatttagtaacttatacatcaaggctctagaatagctcattaggcttaaacccttataatatgatgcataaatttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
                                                     |   |  | | ||||  ||  ||| |  |  | | |    |  | |  | |||  |   |   ||||   |   |  ||   ||  ||   | |  |||  | ||     |||| ||| | |   | |  | | ||||||  |||||||| || || ||||| ||||||||||| |||||||| |||||||| || || || || ||  | || || |||||||| ||||| || 
----------------------------------------------------gtatccataaatatttcatacttta-atttttaagttgattatcatcataatagaatgtgatt-ttatgtaacattcaatgtgttggtttgttcattgattcaattaagtgtttaccttacata--tgttatcttcaagTTTGAATTCCACCATTGTGCCATTATTCGAGAAGGTTCTGAGTGCTAGTGATGCTGGTCGAATTGGTCGTTTGGTCCTCCCAAAAGCATGTGCTGAA

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|5268958|gb|AI770922.1|AI770922
EST:     CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGAGA
genomic: CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA
EST: gi|67040653|gb|CO466908.1|CO466908
EST:     CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA
genomic: CGGTATTGGCCAAGAATAACAGACCAAGAGCTGCAACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA
EST: gi|13150757|gb|BG321079.1|BG321079
EST:     AACAAATATCTGGAGA                         TTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTSA
genomic: AACAAATATCTGGAGAgtatccttga ... attttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgtgtaacagatatagtttttcttttatcttccttgactatattttgcaagTTCAAATTCCACAATCGTTCCATTGTTCGAGAAGGTCCTGAGTGCGAGTGATGCAGGCCGCATAGGGCGCCTTGTTCTTCCAAAAGCTTGTGCCGAG
 ttccttgac  putative branch site 
              atatagtttttctttt  TA-rich tract