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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagcgtcaacgaatcaactttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC

Basic information

species Zea mays
transcript GRMZM2G162251_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G162251_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g38980.2 (Oryza sativa), 3'ss of exon 5
gtcagcgtcaacgaatcaactttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC
|| ||  |||    || |||||| | | |||   |||||     ||   ||     |||||||  |||| ||||  | ||||||||||||||||||| |||||||||||||| ||||| |||||||| ||||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||
gttagt-tcattctattaactttatttggtt---tccatcgg--tctgaagtcctgtgctaatg-ccaaccttcctttttgtagGCTGTCTACTTCGCAGCTTACCTACAGACATTGTATTTGACAATGCTACGGGCATTAGTTTTACATGTGATTTGAGTGACAACATTGCAGCGCCATGGCC

upper sequence: GRMZM2G162251_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G36130.1 (Glycine max), 3'ss of exon 4
------------gtcagcgt-caacgaatcaa--ctttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactat-tgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC
             | |  |  ||   |||  |  |||  |     || ||  ||    |    | | |  ||| | |         |     || |||||||||| ||||||| ||||| |||  |||| |  | ||||||||  |  ||||| ||||||||||||| ||||||||||| || ||||| || || |||||
gaaaaagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaataatgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGAGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCGCCCTGGCC

upper sequence: GRMZM2G162251_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA12G01200.1 (Glycine max), 3'ss of exon 5
------------gtcagcgt-caacgaatcaa--ctttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactat-tgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC
             | |  |  ||   |||  |  |||  |     || ||  ||    |    | | |  ||| | |         |     || |||||||||| ||||||| ||||| |||   ||| |  | ||||||||  |  ||||| ||||||||||||| ||||||||||| || ||||| ||||| |||||
gaaagagctccttttaaagcacagtaaatacatgcttgattcttgtcaattaatattgtattgttggtaaatggtgagactgttgttggttcatatgtagGCTGTTTACTTCGAAGCTTGCCTGGTGATGTGATATTTGACAATTCATCAGGCTTTAGCTTTACATGTGATTTGAGTGATAACATTGCTGCACCCTGGCC

upper sequence: GRMZM2G162251_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv05s0094g00050.t01 (Vitis vinifera), 3'ss of exon 3
---------gtcagcgtcaacgaatcaactttgtctagttcgatccatgcacttccatagcttgatgctaatttccaatcttcactat-------tgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC
           |   |  || |       || || ||   | |   |   | ||   | | |   |   |      ||   |    |        || ||| ||||||||||| ||||| ||| ||||| | |  ||||||||  | |||||| | |||||||| || || |||||||| ||||||||||| ||||||||
tccagtaactcctttgaaaatgccatgttttagtgtatgccaaattaaatatttgtttgggtctgtagaagaaatgaactgtggtcaggtttaaatgcagGATGTCTACTTCGAAGCTTGCCTGCAGATGTGGACTTTGACAATTCAACAGGCTTCAGCTTTACGTGTGACTTGAGTGATAATATTGCAGCTCCATGGCC

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|226431314|gb|GO477650.1|GO477650
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTCTACTTCGGAGCTTACCTACAGATATTGTGT
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGT
EST: gi|211018593|gb|FL002894.1|FL002894
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
EST: gi|78117504|gb|DV535891.1|DV535891
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
EST: gi|67034972|gb|CO463505.1|CO463505
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGATAACGCTACAG
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
EST: gi|211018595|gb|FL002896.1|FL002896
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGATAACGCTACAG
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
EST: gi|50326999|gb|CO522125.1|CO522125
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTTTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
EST: gi|211076051|gb|FL473597.1|FL473597
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG
EST: gi|211018594|gb|FL002895.1|FL002895
EST:     AGCTTGCAAGATTTTGGACAGCAAG                         GCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGATAACGCTACAG
genomic: AGCTTGCAAGATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAG

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: 15 (upstream exon), 49 (downstream exon)
Score: 179

ATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC


Block sizes: 15 (upstream exon), 49 (downstream exon)
Score: 65

ATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC


Block sizes: 15 (upstream exon), 49 (downstream exon)
Score: 66

ATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC


Block sizes: 15 (upstream exon), 49 (downstream exon)
Score: 108

ATTTTGGACAGCAAGgtcagcgtca ... actattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgatccatgcacttccatagcttgatgctaatttccaatcttcactattgtagGCTGTCTACTTCGGAGCTTACCTACAGATATTGTGTTTGACAACGCTACAGGCATTAGCTTTACATGCGATTTGAGTGACAATATTGCAGCACCATGGCC
                           tgctaat  putative branch site (score: 108)
                                        tcttcact  putative PPT
                              taattt  TA-rich tract