Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgattctttatttctttcttccctctcttattcgttcattgtcacttgagttgagtcgttcagactagttgtgttattcctagctaatccaaatctgcacccagttgaatctcatatgatttaattattctttcttcctcctgtggtatcgtgttcgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA

Basic information

species Zea mays
transcript GRMZM2G127379_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g03300.2 (Oryza sativa), 3'ss of exon 1
gtacgtgattctttatttctttcttccctctcttattcgttcattgtcacttgagttgagtcgttcagactagttgtgttattcctagctaatccaaatctgcacccagttgaatctcatatgatttaattattctttcttcctcctgtggtatcgtgttcg---ttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA
                                           |    |  | | |  | ||        ||  | |  ||| | |   | |   |||   | | | | || |||  | |   | | |   | | |  |||    || ||  |  |  |  |   |  | |||  ||||| ||||||||||| || || ||||  |||||||||||  ||||||||||||||||||||||||| |||||||||||||||||||| || |||||
------------------------------------------gtaactaactaact--aatcaccatacatatatatactatccatgtatcaattaaactcg-atcaaatt-aatgccttcaaactgaccaaatttaactttgggctttgaaaatggatatgggatgttgcagGTAAGGCTTTGTTCGGCGAGAACGAATGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGCGCTCGCCCCAACCGCGCCGCCGGCTCGGGGTA

upper sequence: GRMZM2G127379_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g03040.1 (Oryza sativa), 3'ss of exon 1
gtacgtgattctttatttctttcttccctctcttattcgttcattgtcacttgagt-tgagtcgttcagactagttgtgttattcctagctaatccaaatctgcacccagttgaatctcatatgatttaattattctttcttcctcctgtggtatcgtgttcgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA
                            |  || | |   | ||   ||      | | |    | ||       ||| | | |   |    ||| ||||     ||   || || || |    |||||||| ||     ||     || | ||| |  |      | |||  |||||  |||||||||| || || ||||  |||||||||||  ||||||||||||||||||||||||| |||||||||||||||||||| || |||||
---------------------------gtaactaactaactaatcaccatacatatataaactatcca-------tgtatcaattaaactcgatc-aaattaatgcc---ttcaaactgaccaaatttaatt-ttgggctttgaaaatg-gatatggaatgt----tgcagGTAAGGCGCTGTTCGGCGAGAACGAATGGTACTTCTTCAGCCCGAGGGACCGCAAGTACCCCAACGGCGCACGCCCCAACCGCGCCGCCGGCTCGGGGTA
















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|148976344|gb|EE025927.2|EE025927
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|76020928|gb|DT948098.1|DT948098
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|71767924|gb|DR965861.1|DR965861
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|148941938|gb|EC886925.2|EC886925
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|88757969|gb|DY542110.1|DY542110
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|76926936|gb|DV171063.1|DV171063
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|74238117|gb|DT646031.1|DT646031
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|148932878|gb|EE285642.2|EE285642
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|211365730|gb|FL263991.1|FL263991
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
EST: gi|211365728|gb|FL263989.1|FL263989
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTT
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTT
EST: gi|211365729|gb|FL263990.1|FL263990
EST:     CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTG                         CCAAG-CATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC
genomic: CATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACC

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: 43 (upstream exon), 49 (downstream exon)
Score: 256

ATGGTGCACTACCTCATGAGGCAGGCCGCCTCCATGCCGTGCCCCGTCCCCATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 156

ATGGTGCACTACCTCATGAGGCAGGCCGCCTCCATGCCGTGCCCCGTCCCCATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 113

ATGGTGCACTACCTCATGAGGCAGGCCGCCTCCATGCCGTGCCCCGTCCCCATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 17

ATGGTGCACTACCTCATGAGGCAGGCCGCCTCCATGCCGTGCCCCGTCCCCATCATCGCCGAGGTCAACATCTACCAGTGCAACCCCTGGGATCTCCCTGgtacgtgatt ... cgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcatatgatttaattattctttcttcctcctgtggtatcgtgttcgttcttcagCCAAGGCATTGTTCGGCGACAAGGAGTGGTTTTTCTTCAGCCCCCGGGACCGCAAGTACCCCAACGGCGCCCGCCCCAACCGCGCCGCCGGGTCCGGGTA
        atttaat  putative branch site (score: 17)
                                           ttcgttcttc  putative PPT
     atgatttaattattct  TA-rich tract