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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatgttggatttgagaacttttagcttgctatgtttcctttttgtccttttaggagattgtaaacttgactaactagattaaactttatcacttttttgcag

Basic information

species Zea mays
transcript GRMZM2G142984_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G142984_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g38620.1 (Oryza sativa), 5'ss of exon 3
TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatgttggatttgagaacttttagcttgctatgtttcctttttgtccttttaggagattgtaaacttgactaactagattaaactttatcacttttttgcag
||||||||||||||| |||||||||||| ||||||| || || |||||||| || ||  || ||||||||||||||||||| || |||||||||||||||||||||||      | |    |  | ||    |||  | ||   ||||| |  || ||| ||||||  | | |||||||   | || |   |||  |   | ||||||
TGCTATTGAGGGTGGGAAAGAACTTATTGAAGCTTGCAAACCAGCACTTGAATCAGAATATGTCACCAAAGTTATTCATGACTGCAAAAGGGACAGTGAGgtgcctaacccacaactctgaagttattgtagtgcattattatttttttctg-ttctagaagattg--atcctgactaat--ggttgagagttacga---tattgcag

upper sequence: GRMZM2G142984_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA17G34990.1 (Glycine max), 5'ss of exon 3
TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaat--gttggatttgagaacttttagcttgctatgtttcct-ttttgtccttttaggagattgtaaa---cttgactaactagattaaactttatcacttttttgcag---------------------------------------------------------------------
||| ||||| || ||| | || |||||   ||| |||||||| |||||||||||| || | ||||| ||||| ||||||||||| ||| |||||||||||||  || ||   || ||||       |  | ||||||| ||   ||| ||||||   | | | |  ||||  |    ||    ||    |  ||| | | | | |   |||                                                                        
TGCGATTGAAGGGGGAGAGGAGCTTATCATAGCGTGTAAGCCTGCACTTGAGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatttatttgattgctttcttccttgcttgctctggcccctcttttgtatatgttgaaatttgtggaatgtttattcaaaggaaacaaagtgtttgagtggcttgacttgtggtattaggcatttaccattttgtctggccatttaaagctcttataaacttcttgttgtttactag

upper sequence: GRMZM2G142984_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA14G10520.1 (Glycine max), 5'ss of exon 3
TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaat--gttggatttgagaacttttagcttgctatgtttcct-ttttgtccttttaggagattgtaaact--tgactaactagattaaa----ctttatcacttt--tttgcag---------------------------------------------------------------
||| ||||| || ||| | || |||||   ||| |||||||| |||||||||||| || | ||||| ||||| ||||||||||| ||| |||||||||||||  || ||   || ||||       |  | ||||||  || | ||| ||||||   | | | |  ||||  | |  | | | |   ||  |||     || |   | ||   |||  |                                                               
TGCGATTGAAGGGGGAGAGGAGCTTATCATAGCGTGTAAGCCTGCACTTGAGTCTAATTACATCACAAAAGTGATTCATGATTGCAAACGGGACAGTGAGgtctctgatttatttgattgcttgcttccttgcttgccctggtccctcttttgtatatgttgaaatttgtggaatgtttattcaaaggaaaaaaagtgtttgagagccttgacttgtggtcttggcattcaccattttgtctggccatttaaagcacttataaacttcttgttgtttactag

upper sequence: GRMZM2G142984_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT2G25910.2 (Arabidopsis thaliana), 5'ss of exon 3
TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatgttggatttgagaacttttagcttgctatgtttcctttttgtccttttaggagattgtaaacttgactaactagattaaactttatcacttttttgcag
||  || || |||||| | |   ||||  |||| |||||||| ||||| |||||| || | ||||| ||||||||||| ||||| ||  | |||||||||||| || |  ||   ||||   ||||     ||  |||   || |     |  || |||   ||   ||  | ||  |  |   ||  |||  |              
TGTCATCGAAGGTGGAGAGGTGATTATGAAAGCGTGTAAGCCTGCACTCGAGTCTAATTACATCACGAAAGTTATTCACGATTGCAAGCGTGACAGTGAGgtgtctgaactt---tttgttgactt----gttattatagctcatgac-atatttatagtttatgacaacatggataattttttttgtactacag-------------

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|67014473|gb|CO443222.1|CO443222
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|211299166|gb|FL411034.1|FL411034
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTT
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTT
EST: gi|149070923|gb|EE159330.2|EE159330
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|211426112|gb|FL387512.1|FL387512
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCA
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCA
EST: gi|149000223|gb|EE037369.2|EE037369
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|89758395|gb|DY687589.1|DY687589
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|166678610|gb|EG279768.1|EG279768
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCNTAATGTGA
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGA
EST: gi|149102743|gb|EE188274.2|EE188274
EST:     ACTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|67016231|gb|CO444980.1|CO444980
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|148965239|gb|EC906094.2|EC906094
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|211448014|gb|FL403750.1|FL403750
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTATGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|211115805|gb|FL350299.1|FL350299
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|148995982|gb|EE035233.2|EE035233
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG
EST: gi|211487590|gb|FL383666.1|FL383666
EST:     AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAG                         GCTTTGTATTTTCAGTTT
genomic: AGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 167

TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 430

TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 372

TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 317

TGCTATTGAGGGTGGAAAAGAACTTATTCAAGCTTGTAAGCCCGCACTTGAGTCTGATCATATCACCAAAGTTATTCATGATTGTAAAAGGGACAGTGAGgtgcctaatg ... ttttttgcagGCTTTGTATTTTCAGTTTGGCATAAAACTGCATAATGTGATGGATACACAG