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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT

Basic information

species Zea mays
transcript GRMZM2G124151_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os02g07880.1 (Oryza sativa), 3'ss of exon 8
----gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
    || | ||||  |||| || || |||||  ||||    | || | |||||||||||  |||     |||  ||    ||| ||||||||||||| ||||||||||||||  |||| ||||||||||| |||||||||||||| || |||||||||||||||||||| |||||||||   ||||||||||
gtcagtaaataata-ttttgaattgatatttagcttt---cttcttggtcccttgcttttctttc---atatgctttcactttcatcttcagATGGTAGATCCTGGTGGAATCTCTAATTGGTCAGTGACACATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCGTATAGAGCTATTGATGTTACCT

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA14G17110.1 (Glycine max), 3'ss of exon 8
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttctttttta-agtatagttatgttttg-atcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
|| |||   ||     | ||||| | |   || |||| |   |||      || |||   |   ||   | | || |  ||  | || ||||| | |||||||||||||| || || |||||  | ||  ||||||||||||| || ||||||||||||||||||||||  ||||||   ||| |||| |
gtcagtgcacca----atctgttctct--tttaaattgcaatgataggcatctatctcactcgcagctaactcatttggtgtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGATAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGGTCATTCAGAGCTCGGGATATTACAT

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA13G00610.1 (Glycine max), 3'ss of exon 8
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
    || |   |||| || ||| ||     | |  |||  |  | |  || |   |||     | |    |||||| | ||  || ||||||| ||||||||||| || || || |||||| | ||||||||||| ||||| ||| |||||||||| ||||  || || || |||   |||||||| |
----gtgaga-ttttgaattgtaatacagttct--tttgttttaactttttcagccttcagctaattagcttatgtctcgaattt-agATGGTTGATCCTGGTGGCATTGCAAATTGGTCACTAACTCATGTTGACTGGTCTGAGAGAAAATGGCACCCAAAATCTTACAGGGCTCAGGATGTTACTT

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G29670.1 (Glycine max), 3'ss of exon 8
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttctttttta-agtatagttatgttttg-atcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
    || |  |     | ||||| | |   || |||| |   |||       | ||| | | | ||   | |  | || ||  | || ||||| | |||||||||||||| || || ||||| || ||  ||||||||||||| || ||||||||||||||||| ||||  ||||||   ||| |||| |
----gtcagtccaccaatctgttctct--tttaaattgcaatgataggcatttatctatctcacagctaactcgttttgtgtgtatttagATGCTTGATCCTGGTGGAATCGCAAATTGGTCGGTAACATATGTTGATTGGTCTGAAGGAAAATGGCATCCAAGATCATTCAGAGCTCGGGATATTACTT

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: GLYMA17G06790.4 (Glycine max), 3'ss of exon 7
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagta--tagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
            |   || |   |||    |  | ||   | | |  | |  ||     ||||  ||  ||| | |  | |    || ||||||| ||||||||||| || || ||||||||| | ||||||||||||||||| ||| |||||||||| || |  ||||| || |||   |||||||| |
-----------gtgagaatttgaattctaatacagttcttttgttaacatttttcagcctttagctaattagcttttgtctctgatttagATGGTTGATCCTGGTGGCATTGCAAACTGGTCACTAACTCATGTTGATTGGTCTGAGAGAAAATGGCACCCTAAATCATACAGGGCTCAGGATGTTACTT

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT2G19160.1 (Arabidopsis thaliana), 3'ss of exon 8
gttagtaatccttttcaactgttatttgcctttaatttcctcgatccct--tgctttcttttttaa--gtatagttatgttttgat-----cttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
|| || ||| | |||  | | | |   |     || |   |   |   |  | |||||||| |  |   |||| ||||| | ||||        |||||| | ||||||  ||| || ||||||||| | |||||  ||||||||||||| ||| |||| |||||||||||   ||| |   ||| |||| | ||  
gtgag-aattcattttgattctaaagagaaagaaaatgtttgattttttagtactttctttatccataatatacttatggtctgataaatttcgcagATGCTTGATCCTACTGGCATTGCTAACTGGACTGTGACATATGTTGATTGGTCTGAGAGAAAGTGGCATCCAAGAAAATACATGCCTGAAGATATCACGC

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT5G57270.2 (Arabidopsis thaliana), 3'ss of exon 8
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
|| || |     |  ||||| |   |  | |||||   | |  |         || |   ||||  | |  | ||||      |  ||||| | |||||||| |||||  | ||||||||||| ||  ||||||||||||| ||| | | ||||||||||| | ||||||||||    |||||  |  
gtgaggagattataacaactttctct--cttttaaaagctttcactgtgattcttgtcccttaatgaaatctttgttcc---ttaaagATGCTTGATCCTGGAGGAATCTCGAACTGGTCAGTCACATATGTTGATTGGTCTGAGCGTAGATGGCATCCAAAGACATATAGAGCACGCGATGTCTCAC

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: AT4G31350.2 (Arabidopsis thaliana), 3'ss of exon 8
gttagtaatccttttcaactgttatttgcctttaatttcctcgatccct----tgct--ttcttttttaagt--atagttatgttt-------tgatct-------tcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
|| |||  | ||  |    ||    || | |||| |  |||  | || |    | ||  || |  | ||| |  ||  | || | |       ||||||       ||||||| | ||||| | ||||||||| |||||||| || || ||||| |||||||||||||| ||||||||||| | |   || |  ||   |||  | ||  
gtcagttgtactgcttgcttgcgtcttccttttattacccttaagccttaaagtactcattttcctctaacttcatcataatctctccgctcatgatctctttctttcagATGATTGATCCAGATGGAATAGCAAACTGGTCGGTCACACATGTAGATTGGTCCGAGGGCAAATGGCATCCGAAGCTGTACAATGCAAGAGACATCACTC

upper sequence: GRMZM2G124151_T01 (Zea mays), 3'ss of exon 8
lower sequence: PP1S38_381V6.1 (Physcomitrella patens), 3'ss of exon 7
gttagtaatccttttcaactgttatttgcct---ttaattt----cctcgatccct--tgctttctttttta-agtatagttatgttttgatc--ttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
| | ||| |  ||| |  || |  |  || |   |||  ||        ||||| |  || | | || || | || ||   |  | | | |    |||||||| | ||| | |      |  | || ||| | ||||| |||||||||||||| ||||| ||||||||||| | ||| |||       | ||  | ||  
gcttgtattattttgcttctctcttgcgcgtcaattagattaggtttgggatccgtagtgatatattattgacagcatgtgtccgatattactagttcagATGATGGATGCGGCCCACCTTTCAAATTGGACTGTGACCCATGTTGATTGGTCAGAGGGTAAATGGCATCCTAAGTCTTATGAGAAGACTGACATCACGG

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: 45 (upstream exon), 48 (downstream exon)
Score: 87

CCAGCAGAGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCTTCTTCAATgttagtaatc ... tgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 34

CCAGCAGAGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCTTCTTCAATgttagtaatc ... tgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 50

CCAGCAGAGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCTTCTTCAATgttagtaatc ... tgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 68

CCAGCAGAGGGACGCAACTGTATTGCTGATGAGCATTATTTGCCAACCTTCTTCAATgttagtaatc ... tgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT
                                          ttttgat  putative branch site (score: 68)
                                                tcttc  CT-rich tract
                   tttcttttttaagtat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaatccttttcaactgttatttgcctttaatttcctcgatcccttgctttcttttttaagtatagttatgttttgatcttcagATGGTCGATCCTGGTGGAATAGCTAACTGGTCAGTGACTCATGTTGATTGGTCCGAGGGAAAATGGCATCCAAGGTCATATAGAGCTGCAGATGTTACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG