Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgtagttagggttaggttttcctctgcagccagctgctacttccttcgtccttcctatacatacatatatttttctgcttctgatttttatatatatgtataactttgtttgtttcattgattgatcttttcgtgagcag

Basic information

species Zea mays
transcript GRMZM2G052544_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G052544_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g07770.1 (Oryza sativa), 5'ss of exon 2
AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgtagttagg---gttaggttttcctctgc-agccag---ctgctacttccttcg-tccttcctatacatacatatatttttctgcttctg-atttttatat-atatgtataactttgtttgtttc--attgattgatcttttcgtgagcag
||||||| |||||||| ||||||||||| |||||||| ||||| || |||||||||||||||||||||||||| ||||||     |   | ||      |||  || ||| ||    | || ||  ||| | |  |||||  |  |   | ||| | | || ||||  ||| |||| |   |||  |||||   | |||||    ||   |||   | || ||| |||
AGGCGACGCCCAAGACGATCATGAGGGTGATGGGAGTGAAGGGCCTCACCCTCTACCACCTCAAGAGCCATCTCCAGgtaacctagctagctaaccacaccttagctagctagggttttctcctagcttagcttgttcctcgatctctttctatctatatgattctatattcttatgttggatgattaactaaatctgtttttggtttcctgaatatatcatgaacag

upper sequence: GRMZM2G052544_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA08G17400.1 (Glycine max), 5'ss of exon 2
AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgta-gttagggttaggttttcctctgcagccagctgctacttccttcgtccttcctatacatacatatatttttctgcttctgatttttatat-------atatgtataactttgtttgtttcat---------tgattgatcttttcgtgagcag-----------
|||| ||||| || |||||||||||||| ||||| || ||||| || ||||| ||||||||||||||||| || |||||  | |      |  |     | |    |  |||  |  ||      |   |  || | | || | |      ||||   ||  | |  | |       || | | |   | | |||||||  |         | ||| || ||||| |  |              
AGGCCACTCCTAAAACCATCATGAGGGTTATGGGTGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTCCAGgtttgattaatacaaatccatatttctttcatgcttttgattttgctttatgttttagaaacacttttgcgacactgccaatgtctctcgtgttggcttgatgtctctccttctttttgttttttcctttatctttatttattttttcatttgttatctgcatttag

upper sequence: GRMZM2G052544_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G29620.1 (Glycine max), 5'ss of exon 2
AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgt--agttagggttaggttttcctctgcagccagctgctacttccttcgtccttcctatacatacatatatttttctgcttct---gatttttatatatatgtataactttgtttgtttcattgattgatcttttcgtgagcag----------------------
|||| ||||| || || ||||||||||| |||||||| ||||| || ||||| |||||||| |||||||| ||||||||      |         ||   |      |   || ||  | | ||     ||   | || |   |  |    |||  ||||   | | |||   |   | | |    || ||| |  | ||   |     ||  ||||  |                       
AGGCCACTCCTAAAACAATCATGAGGGTTATGGGAGTGAAGGGTCTCACCCTTTACCACCTTAAGAGCCACCTTCAGgttcgaacacaaaccatattcaattaattccacacttcttttacttttcattttatcacacttttgtgaaaccgtctatttctctggctgttttgttgcctctcttttcttctttttcccctttcctttatgttcggtgattaatttattcttctgagtttcatag

upper sequence: GRMZM2G052544_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA15G41740.1 (Glycine max), 5'ss of exon 2
AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgt--agttagggttaggtt--ttcctctgcagcca-gctgctacttcc---ttcgtcct---tcctatacatacatatatttttctgcttctgatttttatatat-----atgtataactttgtttgtttcattgattgatcttttcgtgagcag------------------------------
|||| ||||| || |||||||||||||| ||||| || ||||| || ||||| ||||||||||||||||| ||||||||    |||     |   |  ||    | ||  || |||  |  || |   || |   |   |  || |   || | |||    ||||   ||  | |  | |       |||| |  | || ||| | |  ||  || ||||||   | |                                  
AGGCCACTCCTAAAACCATCATGAGGGTTATGGGGGTGAAGGGTCTCACCCTTTACCACCTCAAGAGCCACCTTCAGgtttgattaatacaaaactatttatatttcattcatgcttttgatttcgattttgctttatgttttagaagcacttttatgacactgccaatgtctctcgtgttggcttgatgtctctccttctttttgtttttcctttatctttattttattttttatttttttcatttgttgtctgcatttag

upper sequence: GRMZM2G052544_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S201_75V6.1 (Physcomitrella patens), 5'ss of exon 2
AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgtagttagggttaggttttcctctgcagccagctgctacttccttcgtccttcctatacatacatatatttttctgcttctgatttttatatatatgtataactttgtttgtttcattgattgatcttttcgtgagcag
|||| || || ||| |  | |||||||| |||||||| ||||| ||||| ||||||||  | ||||||||||| |||||| |          |     | || |   | |||||     | | | | |  ||    |  |           |       |   |  ||  | |||||                                       
AGGCTACACCGAAGTCTGTGATGAGGGTTATGGGAGTGAAGGGTCTTACGCTCTACCATTTGAAGAGCCATCTCCAGgtaatagcaaactcatcagtat-tgtatttatctgctgtcgacgtgg-cttggctggcgaagcggggggacagatttagtaaacgatgttaagtttgtattg-------------------------------------

upper sequence: GRMZM2G052544_T01 (Zea mays), 5'ss of exon 2
lower sequence: PP1S25_131V6.1 (Physcomitrella patens), 5'ss of exon 2
AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgtagttagggttaggttttcctctgcagccagctgctacttccttcgtccttcctatacatacatatatttttctgcttctgatttttatatatatgtataactttgtttgtttcattgattgatcttttcgtgagcag-----
|||| || || ||  |  | ||||| ||||||||||| ||||| ||||| || |||||  | |||||||||||||||||||   |   | |   || ||  |||          | |   ||  |   |  ||    | | | |  | ||  | |     | | |  ||   | |||  | ||  ||     |   ||| || |   | |  |        
AGGCTACACCGAAATCTGTAATGAGAGTCATGGGAGTGAAGGGTCTTACTCTTTACCATTTGAAGAGCCATCTTCAGgtaggctg--ctcgcacttactgcgcatttcatcagcagtaaatt-attaatattacgttttcctcttctctttcgatcacattgtgttcat---tctatggcattcgttaaagtaaacattaatttcgacttagggcttgcag

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: 36 (upstream exon), 38 (downstream exon)
Score: 3

AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgtagttaggg ... tcgtgagcagAAATTCAGGTTAGGGAAGCAGCCGCACAAGGAGTTCAACGAGCACTCGGTTAAGGACG


Block sizes: 33 (upstream exon), 48 (downstream exon)
Score: 20

AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgtagttaggg ... tcgtgagcagAAATTCAGGTTAGGGAAGCAGCCGCACAAGGAGTTCAACGAGCACTCGGTTAAGGACG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 29

AGGCGACTCCCAAGACCATCATGAGGGTCATGGGAGTCAAGGGGCTTACCCTCTACCACCTCAAGAGCCATCTTCAGgtagttaggg ... tcgtgagcagAAATTCAGGTTAGGGAAGCAGCCGCACAAGGAGTTCAACGAGCACTCGGTTAAGGACG