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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG

Basic information

species Zea mays
transcript GRMZM2G088245_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 6
---------------gtaagcatctccttgcaccatcgatcgcattgatg---agtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
                |||  |||||   |  |||| || | | |   |    |||  ||      |  |||  ||  | || |||||||| |||||  | ||||||||||| ||||||||||| ||||| |||||||||||||| ||||||||||| |||||| |||||
gtaagcatcgtttacataaatatctc---gtgccatggacctcttgagtttgcagtaaagaaattgaataatttcaactatctagGTGGTCACTTGGAGCAATCATGTATGAAATGCTAGTGGGCTATCCCCCATTCTATTCTGATGAGCCTATGACAACTTGCAGAAAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: GLYMA10G00830.1 (Glycine max), 3'ss of exon 6
----------------------------------------------gtaagcatctccttgcaccatcgatcgcattgatg-agtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
                                               |   || | |    | |     | |  | || |  | |  | ||| |        | ||| |||||||||||| || ||  |||| |||||||| ||||| ||||| |||||||| || ||||| ||||| || |||   |||||  |||||
gtaatatagaatgtgttttctatttttctgtttcaaaagtctccccatggccacccctccccccttataaacttaatgtttcaatgcattctgatgttgtgtcaatgcttccagGTGGTCTCTAGGAGCTATAATGTATGAAATGCTTGTGGGGTATCCTCCCTTTTATTCAGACGAACCAATGTTGACTTGTAGAAAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: AT3G23310.1 (Arabidopsis thaliana), 3'ss of exon 7
-----------------------------gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
                                    | |   | || |    |   ||||| ||    || | |    |   |    |   |  |||||||| |||||| | ||||||||||| ||||| ||||| | ||| ||||| ||||| |||||||| ||||| |||||  |||||
gtaggtgcagcaaatctgttgggtcttgttctgttttgtttcttcaactcaaaatacattgttgtcgataatttttt-cgggttttcttcctatagGTGGTCACTTGGTGCGATCATGTATGAAATGCTTGTGGGGTTTCCACCATTTTATTCAGACGAGCCAATGACAACTTGTAGAAAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaat-------cccatgtttcca--gGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
                          |    ||     || |   || |   || |  | | | |  ||   | |||||       |   | ||||||  ||||||| |||||| ||||||||||||| ||||| ||||| ||||| || || |||||||| || || ||| | || ||  | |||
agatccttggaactaaaacagagtgatttaaattattatggaaagtc-agaacactccttaattttttccagaccaaattatgattcttttatttccacagGTGGTCACTTGGTGCTATCATGTATGAAATGCTTGTGGGGTATCCACCTTTTTATTCTGATGATCCCATGTCAACATGTAGGAAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 6
-----------------gtaagcatctcct-tgcaccatcgatcgcattgatgagtctagtctcaaacaaatccc-----atgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
                 || | ||||| || ||  |  |    | ||| ||| ||| |  ||  | |   |||       || | ||||||||||| |||||| |||||||||| || ||||| ||||| ||||| || || ||||| || || |||||||| |||||  | |||
gttggttctctaaaactgtcatcatcttctatgatctgttttccccatggattagtttcctcatataaccatctgtttgaatttctccagGTGGTCTCTTGGTGCTATCATGTACGAAATGCTTGTGGGATATCCACCTTTTTATTCAGATGAACCTATGACAACTTGTAGGAAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------gtaagcatctccttgcaccatcgatcgcattgatgag--tctagtc----tcaaacaaatcccatgt--------ttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
                                       |      ||| |       | | |    ||||| |   ||| ||     ||||| |  |   | ||         | ||||||||| |||||  | |||||||| ||||||||||| || || |||||||| || |||||||| |||||||| ||||| || |||
gtatgtgacaagtcgttctcctgaatctttctctttttatccttggctcatgatgtacttgcttagcttgataaagttcttgttgtgttcaaaaaggttgaacgtaagttttcctacagGTGGTCACTTGGAGCAATCATGTACGAGATGCTAGTTGGCTACCCTCCATTTTACTCTGACGAACCTATGACAACTTGTCGCAAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 6
gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
|||||   |   |      || ||    ||  |   |  |  |         ||     ||  | |||||||| |||||  |||| ||||| ||||||||||| || ||||| || |||||||| ||||| || ||| |||||||||| |||
gtaagaggcatttc---tgattgaaaatatctaccggcttgatt-------gatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

upper sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 6
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 6
gtaagcatctccttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
|||||   | | |      || ||    ||  |   |  |  |         ||     ||  | |||||||| |||||  |||| ||||| ||||||||||| || ||||| || |||||||| ||||| || ||| |||||||||| |||
gtaagaggcacttc---tgattgaaaatatctaccggcttgatt-------gatttatggtgcctagGTGGTCTCTTGGAGCTATAATGTACGAGATGCTAGTCGGGTATCCGCCCTTCTATTCCGACGAACCGATGTCTACTTGCCGGAAG

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|71298682|gb|DR785316.1|DR785316
EST:     ATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG                         GTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATT
genomic: ATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatct ... atgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATT




















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 1 RNA-Seqlibrary.


Block sizes: 44 (upstream exon), 13 (downstream exon)
Score: 4

GCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTGgtaagcatct ... atgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaccatcgatcgcattgatgagtctagtctcaaacaaatcccatgtttccagGTGGTCCCTTGGTTCTATCATGTATGAGATGCTAGTGGGTTATCCTCCATTCTATTCTGACGAGCCTATGACTACTTGCCGAAAG
               cattgat  putative branch site (score: 4)
                                              tgtttcc  putative PPT
                                  aaacaaat  TA-rich tract