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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaaatatgaatatttaacttactatatatatgcatgaatcgttgagtaattctatcttttggctcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA

Basic information

species Zea mays
transcript GRMZM2G406553_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------gtatgcaaatatgaata-tttaacttactatatatatgcatgaatcgttgagta----attctatct-----------tttggctcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
                                                           ||||  |||   |||  |||    ||    || ||| |      | ||  ||     ||  ||| |            |||  | ||||  |||||||||||||| || |||||||||||||| ||||| || |||||||||||||||||||||||||| |||||||||||||| |||||| ||||||| ||||||||
gtacgtgaatgcgaatgccttttgctgttgcatatatacctgaccacattccttgtctatatgtgaatgcaaatgctttttactatcgcatgtatactgactacattctgtgtcctatcttatttgattagcaccacttgatttgttttgtatgcagTTGTCCGCACGCTTACTGGACATAGGTCAAACTGCATGTCAGTTGATTTCCATCCTTTTGGAGAATTCTTTGCCTCGGGGTCACTGGACACAAATCTGAA

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 4
----------------------------------------------------gtatgcaaata----tgaatatttaacttactatatatatgcatgaatcgttgag--taattctatcttttggctcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
                                                      ||   ||||       | ||||   | | ||| |  |  ||| |||  || |   | | ||| |   |||    ||||| |  | |||||| |||||||||||||| ||||| || |||||||  ||||| || |||||||||||||| || |||||||| ||||| || || ||||||||||| ||
gtacgcggttgcttgccatttcttttaatggttttaaaacaccaatgaaaaaagatttgaatagtctcacaaatttttttcagtattttcac-cataaattttttaaattgagtctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACTGGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGACACTAATCTTAA

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 4
--------------------------------------------------------gtatgcaaatatgaatatttaacttactatatatatgcatgaatcgttgagt-aattctatcttttggctcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
                                                         |  | |       | | |  | | | ||| | ||      |||  || | |    ||| |   |||    ||||| |  | |||||| |||||||||||  | ||||| || |||||||  ||||| || |||||||||||||| || |||||||| ||||| || || || |||||||| ||
gtatgcagttgcttgccatttcctttaatggttttaaaacaccaatgaaaagagatttgagtagtctcacaaaatatattcattatttttaccataaaatttttaaattggatctttgacttgctatgtttctttggtagTTGTTCGTACTCTTACCAGTCATAGGTCCAATTGTACATCAGTGGACTTCCATCCTTTTGGAGAGTTCTTTGCATCTGGTTCTTTAGATACTAATCTTAA

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 3
--------------------gtatgcaa-atatgaatatttaacttactatatat-atgcatgaatcgttgagtaattctatcttttggc-tcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
                    || |  || ||||||||  |   |||   |||| |  |  |       |  ||  ||| | | || |    | ||||  | |  |||||| || || |||||||| || ||||||||||| || || || || |||||||| |||||||| |||||||| ||||| ||  ||||||| ||||| ||
gtatgcacattagactttgggtgtttaatatatgaattctgttcttttgatatgttgttaaactgatatctagagattttctgttgtaatgtggttttttgtatagTTGTTCGCACGCTTACTGGCCACAGATCAAATTGCATATCTGTGGACTTCCATCCATTTGGGGAGTTCTTTGCATCTGGCTCTCTGGACACAAATCTTAA

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S9_241V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------gtatgcaaatatgaatatttaacttactatata----tatgcatgaatcgttgagtaa----ttctatctt-ttggctcgttt---ccta--tgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
                                                                                    || ||||  |||  ||  |  |      ||       |  | |    |  |   | ||    ||  |||||  || |   |||   |||   ||||||||| || |||||||| || ||| ||||||||||||| ||||| ||||| |||||||| || || ||||| || || || ||  | || || ||||| ||
gtaagcttgttagagctttctctctctctcctccggtccaagtattacatgattaatttgagtttctattccatggtttgtgtggtgtgcacgtattcattctagatcatggatgcgatgcttcgtacttctaatcaggcaaaattttagatcttactgacatttttatacctgggtgcagTTGTACGCACTCTTACAGGTCATCGATCAAATTGTATATCAGTAGATTTTCATCCTTTCGGAGAGTTCTTCGCGTCGGGATCTCTAGATACAAATCTCAA

upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 3
lower sequence: PP1S101_210V6.1 (Physcomitrella patens), 3'ss of exon 3
--------------------------------------------------------------------------gtatgcaaatatgaatatttaacttactatatatatgcat---------gaatcgttgagtaattctatcttttggctcgttt-----cctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
                                                                            |   || |     ||| | ||||   |   | || |||         ||   | ||||    || || |  || | ||| |     |   ||||||||| || |||||||| || ||  |||||||||| || || || |||||||||||||| || || |||||||| || || || ||||| || ||||| ||
gtaagcttgcgaatgtcatctcctaggatatcagttgctttttattaacttgcgttcctattggatggattgtataacataactcattctatcttacttttgacggagatccattgctcttttgatctgatgaggtgctcgat-tactgacccgtataagcgcgagtgcagTTGTACGCACTCTTACAGGTCACCGATCAAATTGCATATCTGTAGATTTCCATCCTTTCGGAGAGTTCTTTGCGTCGGGATCTTTGGATACAAATCTCAA

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: 47 (upstream exon), 49 (downstream exon)
Score: 154

AGTGCTGTGGAGTCGGTTGGTTTTGATTCCACCGAAGTTTTTGTGGCTGCAGGAGCAGCCAGTGGAACAATAAAACTATGGGATTTGGAGGAGGCAAAGAgtatgcaaat ... tcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 67

AGTGCTGTGGAGTCGGTTGGTTTTGATTCCACCGAAGTTTTTGTGGCTGCAGGAGCAGCCAGTGGAACAATAAAACTATGGGATTTGGAGGAGGCAAAGAgtatgcaaat ... tcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 89

AGTGCTGTGGAGTCGGTTGGTTTTGATTCCACCGAAGTTTTTGTGGCTGCAGGAGCAGCCAGTGGAACAATAAAACTATGGGATTTGGAGGAGGCAAAGAgtatgcaaat ... tcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

AGTGCTGTGGAGTCGGTTGGTTTTGATTCCACCGAAGTTTTTGTGGCTGCAGGAGCAGCCAGTGGAACAATAAAACTATGGGATTTGGAGGAGGCAAAGAgtatgcaaat ... tcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatatgcatgaatcgttgagtaattctatcttttggctcgtttcctatgcagTTGTCCGTACTCTTACTGGACATAGATCAAATTGTATGTCAGTTGATTTCCATCCTTTTGGGGAATTCTTTGCCTCTGGGTCATTGGACACTAATCTGAA
                                       ctcgtttcct  CT-rich tract
                       taattctatctttt  TA-rich tract