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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTAAAGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttctgtttattgacaacgttttgcccatgatttggagtatctaagaaactttgcttttccagttgatagaatgtggacatttttttagttttc...

Basic information

species Zea mays
transcript GRMZM2G007915_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G007915_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g16540.1 (Oryza sativa), 5'ss of exon 6
GCTTTAAAGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttctgtttattgacaacgttttgcccatgatttggagtatctaagaaactttgcttttccagttgatagaatgtggacattt---ttttagttttc
||||||||||||||||| ||||| ||||||||||| ||||||||||| || || ||||| | | |    | |  || |  |  | |||   ||||||   |    |     ||| || |  |   |         | |   ||       || |   || 
GCTTTAAAGAGAGCAGAACTTTTTGGTATTTCTGGAGTTACATATTCGTTTACCCAGgtgtctctctaatcttgtgccttc--tctgctagtgatttaatgcgaatcttgtactctggtaataatgcatgagtcctataatcacaccaacttcaacctt-
















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|67018949|gb|CO447698.1|CO447698
EST:     AGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAG                         GGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
genomic: AGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
EST: gi|33099725|gb|CF059685.1|CF059685
EST:     AGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAG                         GGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
genomic: AGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
EST: gi|71439588|gb|DR820638.1|DR820638
EST:     AGAGAGCAGAGCTTTTCNGTATTTCTGGTGTTACATATTCTTTGACACAG                         GGTGTTGTCAAAAATATAATC
genomic: AGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATC
EST: gi|76287586|gb|DV027154.1|DV027154
EST:     TTTCTGGTGTTACATATTCTTTGACACAG                         GGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
genomic: TTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
EST: gi|211475001|gb|FK984421.1|FK984421
EST:     AGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAG                         GGTGTTGTCAAAAATATAATCCMAGMCATTGCATCAACGAATGCAATTATA
genomic: AGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
EST: gi|71431173|gb|DR812223.1|DR812223
EST:     GCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAG                         GGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA
genomic: GCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATA

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), 47 (downstream exon)
Score: 191

GCTTTAAAGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GCTTTAAAGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GCTTTAAAGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

GCTTTAAAGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttc ... tgaatttcagGGTGTTGTCAAAAATATAATCCCAGCCATTGCATCAACGAATGCAATTATATCGGCTGCTTGTGCATTGGAAGCCTTAAAGCTTATTTCTGGGTGCAGCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTAAAGAGAGCAGAGCTTTTCGGTATTTCTGGTGTTACATATTCTTTGACACAGgtttgttttctgtttattgacaacgttttgcccatgatttggagtatctaagaaactttgcttttccagttgatagaatgtggacatttttttagttttc

- - - -  AGAGCA
- - - - - GAGCAG
- - - - - - - AGAGCT
- - - - - - -  GAGCTT