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'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatatccttccctttttagccttgtatagggctttgtgcaaactgaacttctgaagtgacacctttgaaaacaatgaagtactaaatagtttccaactacatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG

Basic information

species Zea mays
transcript GRMZM2G139894_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 15
gtatgatatcct--tccctttttagccttgtatagggctttgtgcaaactgaa-----cttctga-------agtgacacctttgaaaacaatgaagtactaaatagtttccaac-tacatt-----tgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG
||| ||||||||  |  ||| |     |   ||    |||     | ||| ||      | | ||       | ||| |||| |||||||  || |   | | ||  | |||||| ||  ||     | |||||||| ||||| || |||||||| ||||||||||| || || || || |||||||| ||||||||||||||||||||| |||||||||||||||||||||
gtaagatatccttgtttcttgtccatatcaaatgcatcttatcaaatacttaaatatcttgccgaattggatattgatacctatgaaaac--tggaaaccaacatgatatccaacctattttcttgtttcagCATGGTCAAGGAGTCCCTATTGCCGTAAGGCATATCGAATCCATTATTCGGATGTCAGAGGCACATGCAAGGATGCATTTGAGGAGCTACGTGTCTCAGG

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 15
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 14
gtatgatatccttccctttttagccttgtatagggctttgtgcaaactgaacttctgaagtgacacctttgaaaacaatgaagtactaaatagtttccaactacatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG
                              |  | ||||   |   || |  ||  ||  |   ||   |      | |  |  |    ||    |    || ||| |  ||||||| ||||| || || || ||||||||||||||||| ||||| || |||||||| || |||||||| || ||||| || ||     | ||  | ||||
-----------------------------gtgagacttt-cccttgctaa--tttcgagttaggactgatcttgttagttgatcatctcatgacatatc-ctgcatgtttagCATGGACAAGGAGTCCCAATAGCAGTAAGGCATATAGAATCAATGATACGGATGTCTGAAGCACATGCCAGAATGCACCTCAGACAGCATGTTACCCAGG

upper sequence: GRMZM2G139894_T02 (Zea mays), 3'ss of exon 15
lower sequence: PP1S28_266V6.1 (Physcomitrella patens), 3'ss of exon 14
gtatgatatccttccctttttagccttgtatagggctttgtgcaaactgaacttctgaagtgacacctttgaaaacaatgaagtactaaatagtttccaactacatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG
 | |||   |       |   ||  |  | || |  |       ||| ||  |     | |      || ||  ||        | | | | |||      |  ||  ||||   || ||||| || || ||||||||| ||||||| |||||||| || || ||| | |||||||||||| | |||||||| || || |  ||  || |||
-tgtgagcgctgagatatccaaggttgttgtaagaatc---atcaaccgagtt-----atttgttgtttcgatcacctcctcagagtcagt-gttgtttgttgaat--gcagTTCGGACAAGGAGTGCCAATTGCAGTACGGCATATCGAGTCAATGATACGAATGGCAGAGGCACATGCACGCATGCATCTAAGAAGTTTTGTTACTGAGG

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|87153156|gb|DY397945.1|DY397945
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|60340933|gb|DN207906.1|DN207906
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|78125563|gb|DV543947.1|DV543947
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|33093214|gb|CF053208.1|CF053208
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|18450516|gb|BM428794.1|BM428794
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGNGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|78109714|gb|DV528130.1|DV528130
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGCCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCTTCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|18659890|gb|BM500576.1|BM500576
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|32943927|gb|CF048746.1|CF048746
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|19822702|gb|BQ048726.1|BQ048726
EST:     AAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: AAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|32931979|gb|CF036791.1|CF036791
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|32934497|gb|CF039309.1|CF039309
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|60351822|gb|DN218795.1|DN218795
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|18450515|gb|BM428793.1|BM428793
EST:     ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|32932452|gb|CF037264.1|CF037264
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|32932490|gb|CF037302.1|CF037302
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG
EST: gi|211174120|gb|FL130957.1|FL130957
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTTGCAGTAAGGCATATAGAATCAAATCATCC
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATT-GCAGTAAGGCATATAGAGTCAA-TCATCC
EST: gi|32911609|gb|CF016421.1|CF016421
EST:     ATCTAGATAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCT                         CATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAATCAATCATCCGG
genomic: ATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGG

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: 473

ATACATAACCTATGCTAAGCTGAATGTGTTTCCCAAAATACATGATGCCGATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 47

ATACATAACCTATGCTAAGCTGAATGTGTTTCCCAAAATACATGATGCCGATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

ATACATAACCTATGCTAAGCTGAATGTGTTTCCCAAAATACATGATGCCGATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 25

ATACATAACCTATGCTAAGCTGAATGTGTTTCCCAAAATACATGATGCCGATCTAGACAAGATTAGCCATGTTTATGCTGAACTCCGCCGTGAATCCTCTgtatgatatc ... acatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtgacacctttgaaaacaatgaagtactaaatagtttccaactacatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG
                          tactaaa  putative branch site (score: 25)
                             taaatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatatccttccctttttagccttgtatagggctttgtgcaaactgaacttctgaagtgacacctttgaaaacaatgaagtactaaatagtttccaactacatttgcagCATGGCCAAGGGGTTCCTATTGCAGTAAGGCATATAGAGTCAATCATCCGGATGTCGGAGGCACATGCAAGGATGCATCTGAGGAGCTACGTGTCTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT