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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcactaatttgtcactatttctattgcaggtttgcatgatgtcctatttctgcactgagtctttagagtattggctgacatcatgctttctgttcaatcacacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGT

Basic information

species Zea mays
transcript GRMZM2G121128_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G121128_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g42240.1 (Oryza sativa), 3'ss of exon 2
gtaattcactaatttgtcactatttctattgcaggtttgcatgatgtccta-tttctgcact-gagtctttagagtattggctgacatcatgctttctgttcaatcacacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGT
||| ||||||| |||| ||  || | | ||||| ||     ||||||| || || ||||||| ||  ||| ||||| |||||||||||||  || |  ||| |||    || |||||||||| ||||||||||||||| |||| ||| |||||||||||||||||||||| || ||||||||||| |||||||||||||| || |||||||| || 
gtagttcactagtttgacaacatattt-ttgcacgtac---tgatgtcttaattgctgcactagaagcttcagagtgttggctgacatcacactgttggttgaattgttctattagGGCAAAATTGCGCCGTGCTAATTTGCATTTCTTGTCTAAGCCGGTCAAAGATGGGACTACTGGAACTGTGATTGTTCTAACAACTCCAGATGCACAACGA
















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|4730505|gb|AI649671.1|AI649671
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|67023167|gb|CO451916.1|CO451916
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTANGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|148964717|gb|EC905983.2|EC905983
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|76282637|gb|DV022205.1|DV022205
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTATTGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|71433850|gb|DR814900.1|DR814900
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|78117019|gb|DV535406.1|DV535406
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|149086701|gb|EE176240.2|EE176240
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|76915890|gb|DV166152.1|DV166152
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|149090339|gb|EE179645.2|EE179645
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|74244263|gb|DT652177.1|DT652177
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|149107393|gb|EE189272.2|EE189272
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAG
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAG
EST: gi|148963253|gb|EE014242.2|EE014242
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|71448967|gb|DR830017.1|DR830017
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|78091988|gb|DV520362.1|DV520362
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|71319276|gb|DR796401.1|DR796401
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGGGCTAATGTGCACTTCCTGTCTAAGCCGGTCCAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|149073927|gb|EE162255.2|EE162255
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|148935934|gb|EC879984.2|EC879984
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|71448495|gb|DR829545.1|DR829545
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
EST: gi|76019399|gb|DT946569.1|DT946569
EST:     ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAG                         GGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA
genomic: ATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGA

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: 42 (upstream exon), 49 (downstream exon)
Score: 27

CGCTGGCAAGGCTTGGTAGTAGCCAGTCTGCTGGCTACCCTGAGCTTAATATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 70

CGCTGGCAAGGCTTGGTAGTAGCCAGTCTGCTGGCTACCCTGAGCTTAATATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGT


Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 8

CGCTGGCAAGGCTTGGTAGTAGCCAGTCTGCTGGCTACCCTGAGCTTAATATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 25

CGCTGGCAAGGCTTGGTAGTAGCCAGTCTGCTGGCTACCCTGAGCTTAATATTGTGATGGGCGGCAGTGTGGGCAGTGACCCACTAGGTAGTTTCTACAGgtaattcact ... acacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagtctttagagtattggctgacatcatgctttctgttcaatcacacttttagGGCAAAGTTGCGCCGTGCTAATGTGCACTTCCTGTCTAAGCCGGTCAAAGATGGAACAACTGGAACTGTCATTGTTCTAACAACGCCGGATGCACAGCGT
                  ggctgac  putative branch site (score: 25)
                                              cactttt  putative PPT
                                               actttta  TA-rich tract