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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttgctcttctggaatagaactgaattgtggtcagatccatatactagcttgtaggttgaactagtttatttagtgatgtatctgtgatttttagggtattgtgttactctagaatactggatcacttactattttagttgcttaagtatttataattgcctgaaaatatgtttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGTGCATATAACGCTTACATTTCAGCTGCTACCAGGTATGCAACTTTGGGTG

Basic information

species Zea mays
transcript GRMZM2G030902_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030902_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g71770.1 (Oryza sativa), 3'ss of exon 9
gtactttgctcttctggaatagaactgaattgtggtcagatccatatactagcttgtaggttgaactagtttatttagtgatgtatctgtgatttttagggtattgtgtta-ctctagaatactggatcacttactattttagttgcttaagtatttataattgcctgaaaatatgtttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGA---CCATCTCAGGGTGGCTATGGTGCATATAACGCTTACATTTCAGCTGCTACCAGGTATGCAACTTTGGGTG
                                            ||   | |||   | |    ||| |   |||    | || |||    | | |       ||| ||   ||||  | ||  |||     || |   | |  |  ||| ||| || | |   ||||||| |   | || | ||||| ||||| || ||||| || || || ||     |||||||||||||||||||||||||||| || ||||||||||| |||||||| |||||| ||||||   
-------------------------------------------gtacctttgctccaaagc---acttgcc-attggtggctgcatccaatagtatcttatctttgagtaggctctgtagta--ggacattctatttactgaagtagttatgtacttgttaccacctgaaa-tccatctgaaccagGATGAAGAAGTCAGATATCCTCCAAGCAGGGGGGCATCTCAGGGTGGCTATGGTGCATATAATGCATACATTTCAGCAGCTACCAGATATGCAGCTTTGG---
















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|22545757|gb|BU098131.1|BU098131
EST:     CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG                         GAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATG
genomic: CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAGgtactttgct ... tttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATG
EST: gi|149096474|gb|EE182216.2|EE182216
EST:     CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG                         GAGGA-GATGTAAGATACC
genomic: CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAGgtactttgct ... tttgcatcagGAGGAAGATGTAAGATACC
EST: gi|211138007|gb|FL213712.1|FL213712
EST:     CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG                         GAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGG
genomic: CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAGgtactttgct ... tttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGG
EST: gi|21432115|gb|BQ547605.1|BQ547605
EST:     CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG                         GAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGT
genomic: CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAGgtactttgct ... tttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGT
EST: gi|32847027|gb|CD986708.1|CD986708
EST:     CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG                         GAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGT
genomic: CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAGgtactttgct ... tttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGT
EST: gi|26558086|gb|CA830321.1|CA830321
EST:     CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAG                         GAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGT
genomic: CACATGAGCTTGATGGCACAACAGTAGTTGTTGATCGCGCGACTCCGAAGgtactttgct ... tttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactattttagttgcttaagtatttataattgcctgaaaatatgtttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGTGCATATAACGCTTACATTTCAGCTGCTACCAGGTATGCAACTTTGGGTG
 cacttac  putative branch site (score: 2)
     attttagttgcttaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttgctcttctggaatagaactgaattgtggtcagatccatatactagcttgtaggttgaactagtttatttagtgatgtatctgtgatttttagggtattgtgttactctagaatactggatcacttactattttagttgcttaagtatttataattgcctgaaaatatgtttgcatcagGAGGAAGATGTAAGATACCCCCCGAGTAGACCATCTCAGGGTGGCTATGGTGCATATAACGCTTACATTTCAGCTGCTACCAGGTATGCAACTTTGGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT