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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcctaactgctatctgtccagcccaggctgcccagctgatcggacgcctaaaaccaaccttttgtgttggctccgcgttcag

Basic information

species Zea mays
transcript GRMZM2G144372_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 3
ACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcctaactgctatctgtccagcccaggctgcccagctgatcggacgcctaaaaccaaccttttgtgttggctccgcgttcag-----------------
||||||||||||||||||||||||| || ||||||||||| || |||||||||||| | |||||||| || ||||| || ||||||||||||||||||||||| |||  ||  || ||  |  | | |||    | ||  |||   ||  || | |      || || |     |    |  | ||                    
ACAAGATCCGGAGGCAGATCGAGGAGCTAGAGCGCGCCGGGGGTGTCGAGAGTGGGGCTCTCACCGTTGACGGCGTCCCCGTCGACACCTACCTCACCAGgtc-gctcgctcgctcctgcccctgctgcctct-cagcttagcgattccaactcttttgctaaagctctctacctcttccttcctttgcttcttcttcttttctag
















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|211396451|gb|FL097332.1|FL097332
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCC
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCC
EST: gi|71428528|gb|DR809578.1|DR809578
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|67038589|gb|CO464901.1|CO464901
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTTGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|211396455|gb|FL097336.1|FL097336
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|13177876|gb|BG349059.1|BG349059
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAG
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAG
EST: gi|89758156|gb|DY687449.1|DY687449
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|148982506|gb|EE028351.2|EE028351
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|61117886|gb|DN558847.1|DN558847
EST:     TGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: TGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|211396448|gb|FL097329.1|FL097329
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGA
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTG-TGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGA
EST: gi|76012958|gb|DT940128.1|DT940128
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|67023340|gb|CO452089.1|CO452089
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|9824919|gb|BE575016.1|BE575016
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTTGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|211396452|gb|FL097333.1|FL097333
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|116818640|gb|EC861688.1|EC861688
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|211396454|gb|FL097335.1|FL097335
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTAACTCACCAG                         GTTCGTGTGGG
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGG
EST: gi|211396456|gb|FL097337.1|FL097337
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|33104344|gb|CF064304.1|CF064304
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTCGTGTGGGATGAGGGTAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
EST: gi|21987710|gb|BQ779238.1|BQ779238
EST:     AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAG                         GTTTGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT
genomic: AGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 195

ACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

ACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 178

ACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 199

ACAAGATCCGGAGGCAGATCGAGGACCTCGAGCGCGCCGGAGGGGTCGAGAGTGGGACCCTCACCGTCGATGGCGTTCCTGTCGACACCTACCTCACCAGgtctgctgcc ... ccgcgttcagGTTCGTGTGGGATGAGGGCAAATACCCCACAATGTCTCCGCTCAAGGAGATTGTTGGCAGCATCCAGTCACAGGTTGCCAAGATTGAGGATGATATGAAG