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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgctgctgctgcttgtgttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT

Basic information

species Zea mays
transcript GRMZM2G317270_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 6
----------------------------------------------------gtaagcttccaaagaactggtgaaagcaatctgtc-gccatgcatgcttgcttgatctgctgctgctgc-tgcttgtgttgtggatc--cagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                                                     |  | |   |  | | |||| |||    | | |  |  |   |    |  || ||||   | |  | | ||  | || | | ||||  |||| || || ||||| ||||| || || ||  |||||||||||||||| ||||||||||||||||| || || || || || || ||||| | ||| ||  |
gttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaaaatgtgtttataagaaaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
------------------------------------gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgct--tgatctgctgctgctgctgcttgtg--ttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                                     ||  || |   | |  |  | ||| |  | | | |   |   | |||  |  |  |   ||  || |  | | ||    || |   |||||| |  || ||||| ||||| || || ||  |||||||||||||||| |||||||| |||||||| || || || || || || ||||| || || ||  |
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------------------------gtaagcttcca-aagaactggtgaaagcaatctgtcgccatgcatgcttgct--tgatctgctgctgctgctgcttgtgttgtgg--atccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                                                                                          ||| | ||  | |  |  | ||   || |  |     ||  | |||  |  |  |   ||  || |  | | ||| || |    ||||||| |  || ||||| ||||| || || ||  |||||||||||||||| |||||||| |||||||| || || || || || || ||||| || || ||  |
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgct-gctgctgcttgtgttgtgga-tccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
||| | ||   |||||      ||  |||| | |||  | | || | |  | |||    || | |   | |||  | |  |    | |||| || |||||  | || || || ||  || ||||||||||||||||||||||||| || ||||| || ||  | || || ||||| || |||||||||||
gtaggtttagtaagaat--accaattcaatgtctcgaaaagaat-cattttggattccttgtttgacacagctcttatgataatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------gtaagcttccaaagaactggtgaaagca---atctgtcgccatgcatgcttgcttgat--ctgctgctgctgctgcttgtgttgtggatc-cagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
              | ||||      |   |  |  ||      || | |   ||   ||  |  |||  |  ||     | ||  || || |    |   || |||| || ||||| || || || || || ||||| ||||| ||||||||||||||||| || ||||| || || || || || || ||||||||| |||||||
gtaagttaaagaaattagctgattctgtttttattcaaattttcatttttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 4
-----------------------gtaagcttccaaagaactg----gtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgctgctgctgcttgtgttgtggatcc---agGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                        |    ||| ||   |||     ||     |||     |  | |   |  |  |   |  |  |  |  | |   || | ||    |  |   ||| |  |||||||| || || || ||||| |||||||| |||||||||||||| || |||||||| || ||  | || || ||||| || |  || ||  |
gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgtcaaataaacttcttcttttttctccctacattttttttattccttttttttttcaaacacttaagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACCGAGCCACCTACTGATGACTT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 5
----------------------gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgctgctgct--gcttgtgttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                          ||       | | |  | |     |  |   |   |||||| |       |   |   || |  |  | |||   |||||   |||| |  ||||||||||| || || ||||| |||||||| |||||||| ||||| || |||||||| || || ||||| || || ||||| || || ||| |
gtatatagaccctgatgttggctcttgcccattctgtatttatcattttgaatttctgttttgcatgttattcatcttcacctttgttttttgggttgatgtgtggtctcagGAAATGCTCCCCTGACCGCGGTTCAGCTTCTGTGGGTCAACATGATTATGGATACACTGGGAGCACTTGCACTGGCTACTGAACCTCCTAATGATGAGTT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------gtaagcttccaaagaactg----gtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgctgctgctgcttgtgttgtgga---tccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                        |    ||| ||   |||     ||     |||     |  | |   |  |  |   |  |  |  |  | |   || | ||    |   | |||| |  |||||||| || || || ||||| |||||||| |||||||||||||| || |||||||| || ||  | || || ||||| || |  || ||  |
gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgtcaaataaacttcttcttttttctccctacattttttttattccttttttttttcaaacacttcagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACTGAGCCACCTACTGATGACTT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ18007 (Selaginella moellendorffii), 3'ss of exon 3
gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgctgctgctgcttgtgttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                   || | |    |   ||   | |       |  | || ||   ||  | || ||  ||| || |||| |||||  ||||| || || || ||||||||||||||||||||  |||||||||||||| |||| || || || ||||| || ||||| ||||  || || ||
-------------------gtaagattctttactctttaagttcttgggtctcatatgtgactttttcttctcttgtcgttgatc-agGGACGGCTCCGCTCACTGCTGTGCAGCTGCTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT

upper sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ37088 (Selaginella moellendorffii), 3'ss of exon 5
gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgctgctgctgcttgtgttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
                   || | |    |   ||   | |       |  | || ||   |   | || ||  ||| || |||| |||||  ||||| || || || |||||||| |||||||||||  |||||||||||||| |||| || || || ||||| || ||||| ||||  || || ||
-------------------gtaagattctttactctttaagttcttgggtctcatatgtgacattttcttctcttgtcgttgatc-agGGACGGCTCCGCTCACTGCTGTGCAGCTACTGTGGGTGAATCTGATCATGGACACGTTGGGTGCTCTTGCTCTGGCAACCGAGCCACCGACGGATGATCT

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 3 RNA-Seq libraries.


Block sizes: 44 (upstream exon), 26 (downstream exon)
Score: 5

GGGCGATCGGTGTACATCAACATCCAGAAGTTCGTGCAGTTTCAGCTGACAGTCAACGTCGTCGCTCTCGTTGTCAACTTCTCCTCAGCTTGCTTGATAGgtaagcttcc ... gtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT


Block sizes: 27 (upstream exon), 23 (downstream exon)
Score: 1

GGGCGATCGGTGTACATCAACATCCAGAAGTTCGTGCAGTTTCAGCTGACAGTCAACGTCGTCGCTCTCGTTGTCAACTTCTCCTCAGCTTGCTTGATAGgtaagcttcc ... gtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 32

GGGCGATCGGTGTACATCAACATCCAGAAGTTCGTGCAGTTTCAGCTGACAGTCAACGTCGTCGCTCTCGTTGTCAACTTCTCCTCAGCTTGCTTGATAGgtaagcttcc ... gtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgccatgcatgcttgcttgatctgctgctgctgctgcttgtgttgtggatccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
               gcttgat  putative branch site (score: 32)