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

...ccacaccgtgtagtcttattctataaaaacttgaaacagtgacagaatgacgttggcatgctgtctgtctaaacaatttgctattcaattgtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT

Basic information

species Zea mays
transcript GRMZM2G124353_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124353_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g07570.1 (Oryza sativa), 3'ss of exon 1
ccacaccgtgtagtcttattctataaaaacttgaaacagtgacagaatgacgttggcatgctgtctgtctaaacaatttgc-tattcaattgtg---ttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT
  | |      | | |||| |||  || | |    |  | || ||      |||    |  |   | |  |||     ||| | ||   ||||    || |||||| ||||||||||| |||||||||||||| ||||| || ||| |||| |||||||| ||||||||||| || |||||||||||||| || || ||||| |
-aaaaaaaaaaactgttatactagtaagaatc---atggcgaaaggcatgtgtttctgtttttcattttaaaatggaatgcatttttttttgtccattttacagCTGAACATTGTGGAAGGGAAGATGCAGTATCTGTACGATGAGAATGGGAAGAGATACCTCGATTGCTTCGGAGGCATCGTGACAGTTTCATGCGGCCATT
















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|149029600|gb|EE154752.2|EE154752
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|67034943|gb|CO463476.1|CO463476
EST:     AAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAAAAGCCG                         CTCAACATTGTGCAGGGGAAGATGCAGTACCTGTATGACGAGCATGGNGAA
genomic: AAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGG-AAA
EST: gi|149042716|gb|EE047231.2|EE047231
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|148965746|gb|EE016621.2|EE016621
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|20811243|gb|BQ295721.1|BQ295721
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCTATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|148955020|gb|EC900523.2|EC900523
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|31910697|gb|CD651554.1|CD651554
EST:     GCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: GCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|5268428|gb|AI770392.1|AI770392
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|5398767|gb|AI812232.1|AI812232
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|31350579|gb|CD434936.1|CD434936
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|14208236|gb|BG841914.1|BG841914
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
EST: gi|148929128|gb|EC874538.2|EC874538
EST:     AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCG                         CTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG
genomic: AGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAG

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: 256

CTACCGGCCCCGCCCATATGCCGGGCTGGGTGGCGCCGAGATCTTCGAGAAGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 390

CTACCGGCCCCGCCCATATGCCGGGCTGGGTGGCGCCGAGATCTTCGAGAAGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 414

CTACCGGCCCCGCCCATATGCCGGGCTGGGTGGCGCCGAGATCTTCGAGAAGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

CTACCGGCCCCGCCCATATGCCGGGCTGGGTGGCGCCGAGATCTTCGAGAAGAGGAAGGCGGTGCTCGGCCCGTCTCTCTTCCATTACTACCAGAAGCCGgtataccctc ... gtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgacgttggcatgctgtctgtctaaacaatttgctattcaattgtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT
                     gtctaaa  putative branch site (score: 176)
                        taaacaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacaccgtgtagtcttattctataaaaacttgaaacagtgacagaatgacgttggcatgctgtctgtctaaacaatttgctattcaattgtgttcacagCTCAACATTGTGGAGGGGAAGATGCAGTACCTGTATGACGAGCATGGAAAGAGATATCTCGATTGCTTTGGGGGCATCGTGACAGTGTCGTGTGGCCACT

ccacacc
- - - - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ggcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaacaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctatt