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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctccttattatatgacaatgctagagtccatctatctaggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

Basic information

species Zea mays
transcript AC217401.3_FGT001
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g49600.2 (Oryza sativa), 3'ss of exon 2
gtactgctccttattatatgacaatgctagagtccatctatcta-ggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
                    |     ||| | |     | || | ||| |||   |      ||   |||  | |         ||  |||       |    ||   |   |  || ||||      |||||||||  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-------------------aaatgctctaaaatatgcgtgtccaaggtcttacattacatgtaagtgtttccattc--------tccattatctaaaaaaaaagtgtatccattctggaaca------ggaagATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g49600.3 (Oryza sativa), 3'ss of exon 2
gtactgctccttattatatgacaatgctagagtccatctatcta-ggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
                | | |     ||| | |     | || | ||| |||   |      ||   |||  | |         ||  |||       |    ||   |   |  || ||||      |||||||||  | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---------------ctgtaaatgctctaaaatatgcgtgtccaaggtcttacattacatgtaagtgtttccattc--------tccattatctaaaaaaaaagtgtatccattctggaaca------gGAAGATGTTAATCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG

upper sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA09G30910.1 (Glycine max), 3'ss of exon 2
gtactgctccttattatatgacaatgctagagtccatctatctaggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacatttt-cagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
                              ||| ||| |   ||  || ||   || | |  |  | |||   |  |       || ||    || | ||  |      |    |     ||||  ||||||||| | || ||||||   ||  |||||||||||||||||||||| |||||||| |||||||| || || ||| 
----------------------------gaagtacatttgattatattgta-aatgttcattatgtattgtgattgagttgtccctcttgttgttcttctctgctggaataaactctgtaatttgacagGAAGATATAGATCTCATGGCCAGCCTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA

upper sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA07G11310.1 (Glycine max), 3'ss of exon 2
-gtactgc---tccttattatatgacaatgctagagtccatctatctaggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
  || ||    |  | ||||| |        |  | |  | || |     || | ||||||   |||||| |    || |   ||||| ||||  | |||                             ||||||||| | || ||||||   || ||||||||||||||||||||||| |||||||| |||||||| || || ||| 
tatattgtaaatgttcattatgtattgtgattgaattgtacctcttgttcttctctgctggaataaaactat----gtgagctaaagtatgtttaatttga----------------------------cagGAAGATATAGATCTCATGGCCAGCTTGAATTTTGATGCCTACCGGTTCTCAATCTCGTGGTCCAGAATTTTTCCAA

upper sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g02680.t01 (Vitis vinifera), 3'ss of exon 2
gtactgctccttattatatgacaatgctagagtccatctatctaggttttatgctgg-tgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
                        |  |  ||||  | | |  |   | |||      ||    | |||||   |     |||   |   |||  |  | |     ||  ||   ||     ||  ||||||||| | ||||| ||||| ||| | |||||||| || ||||| || |||||||||||||||||||| |||||||
-----------------------gtttttaagtcttttttttaattatatatataatctgtttcatttttgccttgtttcaaatatttgaagaaata-attgaaaactactgatgtg-----ttaacagGAAGATATAGACCTGATGAAGAGTCTTAATTTTGAAGCATACCGCTTCTCAATCTCATGGTCCAGGATTTTCCCAG

upper sequence: AC217401.3_FGT001 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0006g01790.t01 (Vitis vinifera), 3'ss of exon 2
gtactgctccttattatatgacaatgctagagtccatctatctaggttttatgctggtgaaaaacttttgaagtaaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
                 || |  ||| ||  |  |||   |  |  | | ||    ||     ||  ||     |  ||   | || ||  | ||     |  |  | ||||  |      ||| ||||||||| | ||| | ||||||| ||||||||||||||| ||||| ||||| ||||| ||||| ||||| ||||| |
----------------aatcatcatgatattgagcattggttgatatatcataacagt-----accatt----cactagttggcctattccatttag---tatttttattgttgttacctgtttgcagGAAGATCTGGACATAATGAAAATTTTGAATTTTGATGCATACCGATTTTCCATCTCCTGGTCAAGGATTTTCCCTG

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), 32 (downstream exon)
Score: 21

GAAACATTGTATACAATCAGACGGCAGATGTCGCAGTGGATCAATATCATCGCTACAGGgtactgctcc ... acattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG


Block sizes: 49 (upstream exon), 32 (downstream exon)
Score: 32

GAAACATTGTATACAATCAGACGGCAGATGTCGCAGTGGATCAATATCATCGCTACAGGgtactgctcc ... acattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 17

GAAACATTGTATACAATCAGACGGCAGATGTCGCAGTGGATCAATATCATCGCTACAGGgtactgctcc ... acattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG


Block sizes: 43 (upstream exon), 32 (downstream exon)
Score: 15

GAAACATTGTATACAATCAGACGGCAGATGTCGCAGTGGATCAATATCATCGCTACAGGgtactgctcc ... acattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaaagaaagtctgttagacttgtacttggtccttttgtcatgcaacattttcagGAAGATGTCGACCTCATGAAAAGTTTGAATTTTGATGCCTACCGGTTTTCAATCTCATGGTCCAGGATCTTCCCAG
                                              cattttc  CT-rich tract
                                            aacatttt  TA-rich tract