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

...ggtcttacaccgggaaaaatattgttcactccaaactagtttcaaggaatcaggtctttcaacaactaatctttgtgtatttcataatgaaacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA

Basic information

species Zea mays
transcript GRMZM2G001895_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os10g42439.1 (Oryza sativa), 3'ss of exon 19
ggtcttacaccgggaaaaatatt-gttcactccaaactagtttcaaggaatcaggtctttc---aacaactaatctttgtgtatttcataatgaaacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA
    | | | |  |    |  ||  ||||  | |   |  || || ||||||| || | |    || || |||    | |  ||   |  ||||   ||||||||||||| |||||||||||||| |||||||||||||||||||| | |||||| || ||||| || ||||| ||||||||||||||||||||||||||||||
-aaatgataacaaggcttacgttcattcatcctagttt--ttgcatggaatcatgtgtcttgcaaaaaattaacacatattcatca-actatgattgaaaacagGGTTGGCCTTGTTGAAGTACTGCTTGGTATTCTTGATTGGCGAGCTGGTGGCAGGCAGGGACTGTGTAACCAAATGAAGTGGAATGAATCAGAGGCTTCA

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA05G08040.2 (Glycine max), 3'ss of exon 20
ggtcttacaccgggaaaaatattgttcactccaaactagtttcaaggaatcaggtcttt-caacaactaatctttgtgtatttcataatg-aaacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA
  |  |   |   |||| |   ||    ||  ||    || |       | | ||   |  ||  | |    ||| |  | |  ||  || ||||||  ||| ||||||||||||||||| || |||||| ||||||||||| | | ||| |||||  | ||  | |||  ||| ||||||||||||||||| || || || 
-ataatttgctttgaaaca-gctgcatgcttgaagactgtcttgtatgtttatgtgagtataattattctcatttctaaaataaattttgcaaacaatgcagAGTTGGTCTTGTTGAAGTTCTTCTTGGTCTTCTTGATTGGAGGGCTGGCGGAAGGAATGGCTTTTGTTCTCAGATGAAGTGGAATGAATCTGAAGCGTCT

upper sequence: GRMZM2G001895_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA17G12950.1 (Glycine max), 3'ss of exon 20
ggtcttacaccgggaaaaatattgttcactccaaactagtttcaaggaatcaggtctttcaacaactaatctttgtgtatttcataatg-aaacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA
  |||   |     | |  | ||    | | |||||    |             ||| ||     ||     || |  | |  ||  |  ||||||  ||| ||||||||||||||||| || |||||| ||||||| ||| | | |||||||||  | ||  | |||  ||| ||||||||||||||||| || || || 
-ttctgttatatatatattttttaagaattgcaaaccctctctctctctctctctctctctctctctctcaattctaaaataaattttacaaacaatgcagAGTTGGTCTTGTTGAAGTTCTTCTTGGTCTTCTTGACTGGAGGGCTGGTGGAAGGAATGGCTTTTGTTCTCAGATGAAGTGGAATGAATCTGAAGCATCT

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|16927351|gb|BM080420.1|BM080420
EST:     GGCTCGTGATGCTCTTGTTGCACAGGGGCTTAA                         GGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG
genomic: GGCTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG
EST: gi|6012267|gb|AW061809.1|AW061809
EST:     GTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAA                         GGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG
genomic: GTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG
EST: gi|71596430|gb|DR907181.1|DR907181
EST:     CTCGTGATGCTCTTGTTGCACAGGGGCTTAA                         GGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG
genomic: CTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG
EST: gi|89761888|gb|DY689721.1|DY689721
EST:     GTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAA                         GGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG
genomic: GTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGG

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), 45 (downstream exon)
Score: 111

TTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 148

TTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 204

TTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 139

TTGGATGGCAAGGTGGAAGTATACTGGCATTGGAGACATTAAAGCGTGTAGTTGGTGCTGGTAATCGGGCTCGTGATGCTCTTGTTGCACAGGGGCTTAAgtaagctgct ... aacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaatcaggtctttcaacaactaatctttgtgtatttcataatgaaacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA
                  aactaat  putative branch site (score: 139)
                                tatttcataatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggtcttacaccgggaaaaatattgttcactccaaactagtttcaaggaatcaggtctttcaacaactaatctttgtgtatttcataatgaaacaaaacagGGTTGGTCTTGTTGAAGTACTCCTTGGTATTCTTGATTGGCGTGTTGGTGGAAGACAGGGGCTCTGTAATCAAATGAAGTGGAATGAATCAGAGGCTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - aaaaata
- - - - - - - - - - - - - cactcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattt