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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG

Basic information

species Zea mays
transcript GRMZM2G006753_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g10220.1 (Oryza sativa), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactg-gtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG
          ||  ||  ||  |    |||   ||| | ||   | ||| | ||| ||  | || ||      |     | | ||  |||||||| ||    | || ||||| ||| ||||||||| ||  |||||||||||||||| |||||||||||||| || ||||| || ||||||||||||||||| |||| |||||
---------gtggcttacaaaat----ttagtgttgattaattttctatacagaaggcaatgaattgcaagtgaataattgggttccatttctattttaatttggtgcccttgtatgcagGCTTTTTTGTTCAATGATTTGCTCAGATCCAAAGCTTGATTCCCATCGCTTTAAAGATATAATTGATGAGGCAATTGCTGAAG

upper sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA02G31080.1 (Glycine max), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG
                                                   | ||| |  |    ||    |  |   ||  ||  ||    |  ||    ||| |     || | |||||| |||||  ||||| |||| ||||| || || ||||| |||||||| ||||||||||| ||||||||||  || | ||  |
--------------------------------------------------gtaaaaacattgtgatgaggaagaaccttttattggatacagaatttcagtttgatattccctttgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCTCACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

upper sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G12350.1 (Glycine max), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG
                                     | ||| | || |  |||           | ||   | |       ||| | ||  |||| |      |||||||   | |||||| |||||  ||||| |||| ||||| || || ||||| || ||||| ||||||||||| ||||||||||  || | ||  |
------------------------------------gtaaaaacattgtgatgaggaagaaccttttgttggataaag--aatttcagtttgatatcgagtaacttccctt---tgcagGCTATTCTGTTCAATGCTTTGTTCAGATCCTAAACTTGACTCACACCGATTCAAGGATATTATTGATGAGGTTATAGCTGCTG

upper sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G06910.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG
                                       ||  | | |||||      |  | | || |      |   ||  || |||| |||||      | ||  ||||    |||||| |||||| ||||| ||||||| || || ||||||||||| ||||| ||||| || ||  |||||||||| ||||  | ||
-------------------------------------gtaattcatcatcctttcttttcgatattgtt---gaggttgtgagttgatttatatat-----atattttcttcc---cagGCTATTCTGCTCAATGCTTTGCTCGGACCCCAAGCTTGATTCACACCGTTTCAAAGACATGCTTGATGAGGCCATTGCAGCAG

upper sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT3G12170.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaac--aggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG
                              |  ||  |||  || || |  | |    ||| || |     |    | | |||| | ||  |   |||||| | | |  |  |   ||||||||||||||| ||||| |||||||  | || ||||||||||| ||||| ||||| ||||| || |||||||| ||||  |  |
-----------------------------gtaattaatcatccccttgttttcattattgtcaagtttgtgagttgaagtttgtataaacat---tattggtactatatctct---ttcagGCTTTTCTGCTCAATGCTTTGCTCGAACCCCAAGCTTGATTCGCACCGTTTCAAAGATATTATCGATGAGGCCATTGCAGCGG

upper sequence: GRMZM2G006753_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv08s0007g07960.t01 (Vitis vinifera), 3'ss of exon 5
gtgatttctttgaattttaatttccttttatgcttgttcaaacctttatcctgaaagctgtaaactggtccaacaggcttgttttaattt-ctatattggcat----tgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG
                                              ||   |   |  |||       | |       || |||    || |   ||  || |    | | |  | ||  |||||||||||||  ||||| |||| || || || ||||| ||||| ||||| |||||||||||  |||||||||| ||    | ||
---------------------------------------------gtacaatagcaaatgtgtttcccttctttttttttttttaggcttgccggatcagcctctaatctgctttccttctcagGCTTTTCTGTTCAATGCTTTGTTCTGACCCTAAGCTGGATTCACACCGATTCAAGGATATTCTTGATGAGGCAATATCAGCAG

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: 49 (upstream exon), 26 (downstream exon)
Score: 99

AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACATgtgatttctt ... ttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG


Block sizes: 41 (upstream exon), 21 (downstream exon)
Score: 10

AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACATgtgatttctt ... ttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG


Block sizes: 47 (upstream exon), 24 (downstream exon)
Score: 15

AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACATgtgatttctt ... ttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG


Block sizes: 49 (upstream exon), 26 (downstream exon)
Score: 33

AGGCTGACATTGAAGAATTTGAAGCTAAATATAGAGGGTCAGATTCTGAGAAAACGGACTTGAAGGAACTCTACACAAAATATAAGGGCAACATGAACATgtgatttctt ... ttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggtccaacaggcttgttttaatttctatattggcattgttcccttctattcagGCTTTTCTGCACAATGATTTGCTCAGAACCAAAGCTTGATTCTCACCGCTTCAAGGATATAATTGATGAGGCGATTGGTGAAG
                 ttttaat  putative branch site (score: 33)
                                     ttgttcccttctattc  putative PPT
              ttgttttaatttctat  TA-rich tract