Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatccaaaatccagagataacaactttgaataaataagaaaacttacaattaattttcatggcag

Basic information

species Zea mays
transcript GRMZM2G101438_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g52420.1 (Oryza sativa), 5'ss of exon 4
ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatccaaaatccagagataaca-------actttgaataaataagaaaacttacaattaattttcatggcag---
||| ||||| || ||||||||||| || |  ||||||||||||||||| ||||||||||| |||||||||||||| || || ||||||||||| ||||| ||||||||||||||||   |||||||||       |||    | | ||||||||  |   |||| |  | | | |      
ATACCCTTCGCCACTTGGTTATTGCGGTTTTCCAAAGAGTGTCTGCACCTCAGTGAATGAGTGCATCTGTCATGGTATACCTGATTCTCGTCCTCTTGAAgtaagccatccaaaatt-ggagataacacacacatactgcatacatataagaaagttacaaattgacctcctttgttacag

upper sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA01G39200.1 (Glycine max), 5'ss of exon 4
ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagcc-atccaaaatcc---agagataacaactttgaataaataagaaaacttacaattaattttcatg-gcag
||| || || ||||| || ||| || | |  || |||||||||||||| || || ||||||||||| || ||||| || || ||||| ||| ||||||||||    | || |||  ||      || |||  |   ||  | || || ||    |  |   | | || ||  ||||
ATACCCATCTCCTCTCGGCTATGGTAGTTTTCCTAAGAGTGTCTGCACATCTGTAAATGAATGCATTTGCCATGGAATACCAGATTCCCGTGCCCTTGAGgttcttctatacaagttcttttgaagttaaacatcctgtgtgaaaaaaaatttgttgacacattctttatttgcag

upper sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 4
lower sequence: AT4G37040.1 (Arabidopsis thaliana), 5'ss of exon 4
ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatccaaaa-------tccagagat--aacaactttgaataaata------agaaaacttacaa-----ttaattttcatggcag
 |||||||| |||||||||||| | || | ||| || ||||| ||||| || |||||||||||||| || ||||| || || |||||  | || ||||||||  ||  |   |||       |  || |    ||||  |||  ||   |       |  || ||||  |     ||  ||    ||||||
TTATCCTTCGCCTCTTGGTTATGGAGGTTTCCCGAAAAGTGTTTGCACATCTGTGAATGAATGCATTTGCCATGGTATACCAGATTCAAGACCACTTGAGgtgcgcttttttaaaaggtgtttgtaggggctaaacagatttttatctctgtcccttatgaatcttaataatgtattgtttcctttggcag

upper sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 4
lower sequence: Vv07s0031g00820.t01 (Vitis vinifera), 5'ss of exon 4
ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatcc---aaaatccagagataacaactttgaataaataagaaaacttacaattaattt-tcatggcag-----------------------
 || ||||| || || || ||| ||||||  |||||||| |||||||| ||||||||||||||||| || ||||| || || ||||| ||||| ||||||||      | |   |  |   |||  |    |    |  |   ||||  |   |    |||| |  |||   ||                        
GTACCCTTCCCCCCTAGGCTATGGTGGATTTCCAAAGAGCGTCTGCACATCAGTGAATGAATGCATTTGCCATGGAATACCAGATTCCCGTCCACTTGAGgtctattttacttaaggacttagatttcttgagccagtgtggttaagtcattgtgtttttaagtagtcaaatcacttatacaaaattgtcatttgcag

upper sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 4
lower sequence: PP1S90_139V6.2 (Physcomitrella patens), 5'ss of exon 4
ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagcc---atccaaaatccagagataaca-actttgaataaataagaaaacttacaattaattttcatggcag-------------------------
 |||||||| |||||||||||| |  | |  |||||||| || || || || || ||||| |||||||||||||| ||||| || || ||||| ||||||||  |     |   | |||| || | |  |     | ||| |  || |||    |  |   |   |   ||  ||                         
TTATCCTTCTCCTCTTGGTTATGGAAGTTTTCCAAAGAGCGTTTGTACCTCTGTAAATGAGTGCATCTGTCATGGCATTCCTGACTCCCGTCCACTTGAGgttggtttggaaatacaatctagtgctctcttgggtcgaaaacttatgaaccgctctagcgaccctgggtgatagtgcgaagtcttagtttgctggtcac

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|148995508|gb|EE034697.2|EE034697
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|76912468|gb|DV164746.1|DV164746
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|78075681|gb|DV504115.1|DV504115
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|78075680|gb|DV504114.1|DV504114
EST:     GATTCCGGATTCTCGTCCCCTTGAG                         GAGGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: GATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|101399011|gb|EB821378.1|EB821378
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|71436246|gb|DR817296.1|DR817296
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|116819988|gb|EC863161.1|EC863161
EST:     CAGTGAATGAATGCATCTGTCATGGCATTCCGGATTCTCGTCCCCTTGAG                         GATGAAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
EST: gi|76289409|gb|DV028977.1|DV028977
EST:     CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAG                         GATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT
genomic: CAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT

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

ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 36

ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 34

ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 39

ATATCCTTCACCTCTTGGTTATTGTGGATACCCAAAGAGTGTCTGCACTTCAGTGAATGAATGCATCTGTCATGGGATTCCGGATTCTCGTCCCCTTGAGgtaagccatc ... ttcatggcagGATGGAGATATCATCAATATTGATGTTACTGTCTACCTCAAT