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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacctctgtactgtatttaaataatgtatcttagtgtgccttttctgttaggtgttgtttggttcacggaatatcatgtaaatggtaataagttt...

Basic information

species Zea mays
transcript GRMZM2G134396_T03
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os07g49270.1 (Oryza sativa), 5'ss of exon 19
TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacctctgtactg---tatttaaataatgtatcttagtgtgccttttctgttag-gtgttgtttggttcacggaatatcat--gtaaatggtaataagttt
|| |||||||| |||||||||||||||| ||| ||||  || ||||||||||| ||||||||||||||||||||||||||| ||||||| ||||||||||||||||| || |||||    | | |   |   || |  |    | || |   ||| ||   |||  ||  |    | |||  | |  || | |||     ||   
TCACACTGGATTGGGAGAAACTACTACAAAAGAGGTCATGATGGCAATGACATTCACCAGACAAATGTTCCTCACATCAGGATTGAATTCCGACACACTgtatgtacttc-gtactagcttctctgcctggagtctgatctcttcccgtacttgtcagcacgtttgtttctgttggtaattgcgtttgttactggcccgcag---

upper sequence: GRMZM2G134396_T03 (Zea mays), 5'ss of exon 18
lower sequence: PP1S168_82V6.1 (Physcomitrella patens), 5'ss of exon 18
TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacctctgtactgtatttaaataatgtatcttagtgtgccttttc---tgttaggtgt-tgtttggttcacggaatatcatgtaaatggtaa--taagttt------------------------------------
|| |||||| | || |  || || |||| ||||||||| ||||||||||| |||||  |||||||||| ||||||||  | || || || || ||    || || |    |   ||   ||||     || | |  | | |    || |   | |||| | | || | ||| ||     | |    |||||       | |||||                                    
TCGCACTGGCTTGGAAAGAATTATTACAAAAGGGGTCCTGAGGGCAATGATATCCATAAGACAAATGTCCCTCACATGCGCGTGGAGTTCCGTCATCAGgtgtgaaatcata-gcttcttttactgcttgcaacccattctatagttacgcattttagatatatgatgggtacattttgtttgtcataaatctctggtttagtttctggttggatgctcatgagtctatgttgtcctgcag
















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|14203330|gb|BG837007.1|BG837007
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAACTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|67028452|gb|CO457201.1|CO457201
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGNTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|16925558|gb|BM078626.1|BM078626
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|161590017|gb|EY959294.1|EY959294
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATAC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATAC
EST: gi|78026552|gb|DV494939.1|DV494939
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAACTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|211360498|gb|FL383506.1|FL383506
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|50336749|gb|CO531875.1|CO531875
EST:     ACATCCCCCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATTTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|71299097|gb|DR785545.1|DR785545
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|149090162|gb|EE179462.2|EE179462
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|24769083|gb|CA404212.1|CA404212
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACCCACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|33090962|gb|CF050956.1|CF050956
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGGAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|78121620|gb|DV540004.1|DV540004
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|211281929|gb|FL464725.1|FL464725
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|4885898|gb|AI677018.1|AI677018
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAACTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|211424040|gb|FL301692.1|FL301692
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
EST: gi|71772852|gb|DR970775.1|DR970775
EST:     ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACT                         ATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC
genomic: ACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCC

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), 46 (downstream exon)
Score: 161

TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCCGAAGAAGTTGACAGGTGAAGAGCAGGGGAATTGCAGTGAAGTCTGGCGG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 144

TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCCGAAGAAGTTGACAGGTGAAGAGCAGGGGAATTGCAGTGAAGTCTGGCGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 335

TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCCGAAGAAGTTGACAGGTGAAGAGCAGGGGAATTGCAGTGAAGTCTGGCGG


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 116

TCTCACTGGATCGGGAGAAACTACTACAGAAGGGGTCCGGAGGGCAATGACATCCACCAGACAAATGTTCCTCACATCAGGGTTGAATTTCGACACACTgtatgtacct ... tcgactgcagATCTGGAAAGAAGAAATGGAGCTGATACATTTTGGAAATGTTAACCTACCCGAAGAAGTTGACAGGTGAAGAGCAGGGGAATTGCAGTGAAGTCTGGCGG