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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtctcacctgaacccacttaaaacatgcatggatgtttttctgtaatatgcttttgttttgttttttccctgaaagatacttttgaaccttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG

Basic information

species Zea mays
transcript GRMZM2G062024_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G062024_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os04g44430.1 (Oryza sativa), 3'ss of exon 12
tggtctcacctgaacccacttaaaacatgcatggatgtttttctgtaatatgcttttgttttgtttttt-ccctgaaagatact-tttgaacctt---aatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG
   |  |||   ||  ||   || || | | |  |||    |   |  |  |  ||  |  ||||     | |       ||||  |||||| |    |||||||||||||||| |||| |||||  | ||||||||||  |||||||| ||||| |||  ||| | | | || ||||| ||||
---tgacactgaaatgcatccaatacctcc-taaatgacagttaatt-tgggtattcatcgtgttcaaagctcatggttttactgcttgaacttgttgaatgcagGACAAAATCCATAACTGGAGATCGACAGCTCTTACCTTGACATCTATCCTCTTCATTGCAGCTATATTTTGGTTTATTG
















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|32840593|gb|CD980274.1|CD980274
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840289|gb|CD979970.1|CD979970
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840250|gb|CD979931.1|CD979931
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|6012686|gb|AW062123.1|AW062123
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|91875800|gb|EB405757.1|EB405757
EST:     CTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: CTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840295|gb|CD979976.1|CD979976
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGACCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840590|gb|CD980271.1|CD980271
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|211124332|gb|FL444268.1|FL444268
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCMCAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840308|gb|CD979989.1|CD979989
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|5108252|gb|AI739965.1|AI739965
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|74236979|gb|DT644893.1|DT644893
EST:     TTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840674|gb|CD980355.1|CD980355
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|29545180|gb|CB605358.1|CB605358
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840071|gb|CD979752.1|CD979752
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGGCATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840235|gb|CD979916.1|CD979916
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
EST: gi|32840128|gb|CD979809.1|CD979809
EST:     TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAG                         GACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT
genomic: TCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTT

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: 123

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 91

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 104

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 160

CGTGAAGCCACATTTGCGGCCATTGGCAATGGCCGTATCCACTGTTTCAATCCATATATTTGGCGATGTGCCTTCTTCACCTCTTGTTGGGCTTCTTCAGgtgcttcttc ... cttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatatgcttttgttttgttttttccctgaaagatacttttgaaccttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG
                                            ccttaat  putative branch site (score: 160)
        ttttgttttgtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtctcacctgaacccacttaaaacatgcatggatgtttttctgtaatatgcttttgttttgttttttccctgaaagatacttttgaaccttaatgcagGACAAAATCAATAATTGGAGGGCCACAGCTCTTATTTTGACATCCATCCTTTTCGCTGCTGTTGTGTTCTGGTTCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - -ctgaacc
- - - - - - - - - - - - - -tgcatgg
- - - - - - - - - - - - - - - - - - - ttttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaagata