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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgaaggattgccagtttgtgtgttattcaagtaatcttggttcaaaaatagagctaacaagtaacattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA

Basic information

species Zea mays
transcript GRMZM2G423861_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os04g57140.1 (Oryza sativa), 3'ss of exon 6
-----------------gtactgaaggattgccagtttgtgtgttattcaagtaatcttggttcaaaaatagagctaacaagtaacattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
                   | |||||   ||||| ||  |  ||||   ||||||| ||| |||      || ||| || | ||  |||| | ||||||| ||||||||||| ||||| ||||||||||| || || |||||||||||| |||| || |||||||||||||| ||||| || ||||| ||  | ||||
gtactggcctgggcagctgattgaagtgctgccaattcttacgttacagaagtaatattgtttccttggaagtgctgactaatataattgctatgcagTTACAACATGATTATATTTTAGGAAACTATCCAGTAGGTAGGGATGATGCTGCACAGCTATCTGCTCTGCAAATATTGGTCGAAATTGGCTTTGTTGACA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA11G09480.1 (Glycine max), 3'ss of exon 8
------------------gtactg--aaggattgccagtttgtgt-gttattcaagtaatct-----tggttcaaaaatagagc-taacaagta-----acattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
                  || ||   || || |   ||| | | | |||||| ||  || ||     |   |  || |||   | | |   ||      |   | |  | |||||||| ||||| || |||||||| || || ||| |||| ||| |||||||  | || || |||||  |||||||||||| ||||||||||||  |    |
gtatgtctttttgtttctgttctatcaatgaataagagtatatcttgttattgaataaaactgcaattaccttcaagatattacatcattggtgcatggatgctttgttacagTTGCAGCATGACTATATTTTGGGTAATTACCCTATTGGAAGGAATGATGCAGCCCAGCTTTCTGCATTGCAAATCTTGGCTGAGATTGGATTTGTTAGAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA16G21340.1 (Glycine max), 3'ss of exon 11
------------------gtactgaaggattgccagtttgtgtgttattcaagtaatcttggttcaaa--aatagagctaacaagtaacattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
                    ||| ||| ||| | || ||   | | ||     |||| |  |  || |  | |   | | | |    |  |  |  | ||| ||||||||||||| ||||||||||| || |||||||| |||||||||||| | || || |||||  | |||||||| | ||||||||||||  |   ||
aaagataaagaaataagacaactaaagaatt-caagattagatatgataatcctaatttgtgaccatatcatttttgttgatactggatgtgttggtacagATGCAACATGATTATATTTTGGGAAATTACCCTGTTGGAAGGGATGATGCTGCTCAGCTTTCTGCCTTACAAATCTTAGCTGAGATTGGATTTCTTAGCA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA01G35950.1 (Glycine max), 3'ss of exon 8
------------------gtact--gaaggattgccagtttgtgt-gttattcaagtaatct-----tggttcaaaaatagagc-taacaagta-----acattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
                  || ||  ||| || |   ||| | | | |||||| ||  || ||     |   |  || |||   | | |   ||      |  |  |  | |||||||| |||||||| |||||||| || || ||| |||| |||||||||||| | || || |||||  |||||||||||| ||||||||||||  |    |
gtatgcattcttatttctgttctatgaatgaataagagtatatcttgttattgaataaaactgcaattaccttgaagatattacatcattggtgcatggatgtattgttacagTTGCAGCATGATTATATTTTGGGTAATTACCCTATTGGAAGGGATGATGCTGCCCAGCTTTCTGCATTGCAAATCTTGGCTGAGATTGGATTTGTTAGAA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA09G32740.1 (Glycine max), 3'ss of exon 8
---------------------------gtactga--aggattgccagtttgtgtgtta---ttcaagtaatcttggttcaaaaatagagctaacaagtaacattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
                            |  |||  || ||  | ||||| |||   |   | ||| ||   |    | | | ||   ||| | |    |  |  |  | ||| ||||||||||||| ||||||||||| || ||| |||| |||||||||||| | || ||||||||  | ||||| |||| ||||||||||||  || |||
gtatgccttttcattatgaaaccttacctgatgacaagtatatctagtttatgtacaaagctgcaattaccttcaagttatagattt-gctgatactggatgtgttgttacagATGCAACATGATTATATTTTGGGAAATTACCCTATTGGAAGGGATGATGCTGCTCAGCTCTCTGCATTACAAATTTTGGCTGAGATTGGATTTCTCAACA

upper sequence: GRMZM2G423861_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv04s0044g02020.t01 (Vitis vinifera), 3'ss of exon 7
--------------------------------------------------------gtactgaag-gattgccagtttgtgtgttattcaagtaatct-tggttcaaaaatagagctaacaagtaac-attgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
                                                        ||||      || |  |  |  |  | ||   || | | | | || || ||   | || |||||  ||    ||||||   |||||||||||||| || || ||||| || ||||||||||| || ||||||||| ||||||| |||||  |||| || ||| |||||||||||||||| |   
gtatgtaatcttattttaaagtaatttgtgagcaactctgattaatatttgaatatgtacaactttgactaactatgggaattttgaacaggcagtatctgatttaagctttgatctaacttgtttttattgttt--cagTTGCAACATGACTATATATTGGGCAATTATCCTGTTGGAAGAGATGATGCTGCACAACTATCTGCATTGCAGATTTTGATTGAGATTGGATTCATTGGTT

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), 49 (downstream exon)
Score: 126

AGAAATTCTTCATTGCAAACTTGTATTCAAGAAACGTCTCTTCCGCGAGTCGGATGAGGCTGTGACTGATCCAATGTTTGTTCAGCTATCATATGTCCAGgtactgaagg ... tgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

AGAAATTCTTCATTGCAAACTTGTATTCAAGAAACGTCTCTTCCGCGAGTCGGATGAGGCTGTGACTGATCCAATGTTTGTTCAGCTATCATATGTCCAGgtactgaagg ... tgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA


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

AGAAATTCTTCATTGCAAACTTGTATTCAAGAAACGTCTCTTCCGCGAGTCGGATGAGGCTGTGACTGATCCAATGTTTGTTCAGCTATCATATGTCCAGgtactgaagg ... tgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

AGAAATTCTTCATTGCAAACTTGTATTCAAGAAACGTCTCTTCCGCGAGTCGGATGAGGCTGTGACTGATCCAATGTTTGTTCAGCTATCATATGTCCAGgtactgaagg ... tgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattcaagtaatcttggttcaaaaatagagctaacaagtaacattgttctgcagTTGCAACATGATTACATTTTGGGAAACTATCCTGTTGGCAGGGATGATGCTTCACAACTCTCTGCTCTGCAAATCTTGGTTGAGATTGGATTCATCGACA
                                    aagtaac  putative branch site (score: 77)
                                            ttgttct  CT-rich tract
                  ttcaaaaata  TA-rich tract