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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacagtgttattgttcattgcacaaataactcctatcagcattttgcatttttctcattgtttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG

Basic information

species Zea mays
transcript GRMZM2G178546_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 3
gtatacagtgttattgttcat-tgcacaa-ataactcctatcagcattttgcattttt--ctcattgtt-----------------------tcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG---
   ||  |  ||  ||||||  || | || |   | |||   | | ||||||||||||  ||| |||||                       |  |||||||||||||||||||||| |||| |||| |||| ||||||||||| ||||||||||| || ||||| |||||||||||| ||   || || | |||   |    
--gtaaggaatttatgttcacatgtaaaatactccccctgctaaccttttgcatttttcactctttgttgactctctcttatgtgtgttttgttctttagGTTTTTGACTTTGTGAAACTAACTGAACTGTATTACGCTGGAAGTCATGGAATGGATATCATGGGGCCTGTTAGGAAGTCT---GATTCGAGTGGTCAGCATG

upper sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA09G36570.2 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------gtat-acagtgt-tattgttcattgcacaaataactcctatcagcattttgcatt---tttctcattgtttctttt-----agGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG
                                                                    | |  || |  |  | |  |  |  ||  ||     | | ||||    | |   |   ||||  |||    || ||     |||| | | | |||||    ||||  ||| | || |||||||| || |||||||||||||| || |||||||||||  |  ||         |||  | |  
gtagttgaacaatttttagaaaaacacatacaattttctatctctttttaattcccttatctatctgagcaccactgcatacactcctgctcccaagaagcttccttgtcagttgctggttctaactttcgtattaccgctgttggctcagGTATATCAATTTGTAGGACTAACAGAACTTTATTACGCTGGTAGTCATGGAATGGACATCATTGGCCCTGTTAGACAATCTGTATCTGATAATCACCTAA

upper sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv16s0022g00660.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------gtatacagtgttattgttcattgcacaaataactcct-atcagcatt---ttgc-atttttctcattgtttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG
                                                             ||  | | | | | ||| ||  | | ||   |  | |||  || |   |||  |  |  |  | | || | ||||||| | | | ||||||   ||||  ||  | ||||||||||| || ||||| |||||||| ||||||||||| ||  |  | | |       |        
gtaattggcaggcttttgagtgtgtgctattattttaaaatcattatggcaatttcctcccattta-tatcagttttccttctatagatggtttttcatcttcactgacttgttacgtaacctactatt-catttagGTGTATAATTTTGTGGGACTAACAGAGCTCTACTACGCTGGTAGTCATGGGATGGACATCATGGGCCCTGTCAGACACTCCATTTCTAATGACCATCCAA

upper sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S141_116V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------------------------------------gtatacagtgttattgttcattgcacaa--ataactcctatcagcattttgcatttttctcattgtttcttt---tagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG
                                                                                              |||| | ||| | ||  ||  |  |   | | || |  || |    ||      | | | | | | |||    |||| |  || |||||| | ||    |||||||||||||| ||||| ||||||||||| |||||||| ||||  |  |   | | ||  |  || | |   |
gtgaggcttcggtcgttcttttcatagcagtttcctcggtcatggaaaatatttagtgggtggccatcgtacttcaattcttccttcgcattggtacatttttaattttttttttatcatagtgattcatgccaactgaatgtgggcgtattactctatttttgaacagGTATACGATTTTGTGCAACTGTCGGAATTGTACTACGCGGGAAGTCATGGAATGGATATAATGGGTCCTGCGAAAAGTTCAAGTGGTTTTAAAGTCAACG

upper sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S47_110V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------------------------------------------------------------------------------------gtatacagtgttattgttcattgcacaaataactcctatcagcattttgcatttttctcattgtttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG
                                                                                                       | |    | || || ||  ||        |||      ||  ||     | || |   |||   |     ||||||  || |||||| |  |    || |||||||| |||||||| ||||||||||| |||||||| ||||  |  |   | | ||  |  || | |   |
gtgagtctttggtccgtcgtttctctatgtagtcgaaaacgttgtgtggatgaccattgtacttaagtctttcaattattctcggcattttgcttcgttttttttttttcttttttttttttttttttgctgaacataacccaatatcggtgaattgttcgatt--ctgaaacagGTTTACGATTTTGTGCAATTGTCGGAGTTGTACTATGCTGGAAGTCATGGAATGGATATAATGGGTCCTGCAAAAAGTTCAAGTGGTTTTAAAGTCAACG

upper sequence: GRMZM2G178546_T01 (Zea mays), 3'ss of exon 4
lower sequence: PP1S201_97V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------gtatacagtgttattgttcattgcacaaataactcctatcagcattttgcatttttctcattgtttctttt------agGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG
                                     | | || || ||   ||     ||     |      | |  | |||  ||||   | | |||||||  | |      |||| |  || |||||| | ||    || |||||||| || ||||| |||||||||||||||||||| ||||  |  |   | | ||  | |||   |   |
gtcagcatgatcttcaaaactgttttctaccatccttgaaaac-gttttgaggtctggggcctgtgtg-tgtgtgtgtgaattgagcatggat-taattgttttatattgaaacagGTCTACGAATTTGTGCAACTGTCCGAGTTGTACTATGCGGGAAGTCATGGAATGGACATAATGGGTCCTGCAAATAGCGCAAGTGTTTTCAAGATCAATG

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|149101959|gb|EE287477.2|EE287477
EST:     CGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAG                         GTTTTTGACTTTGTGAAGCTAAATGAATTGTACTA
genomic: CGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAGgtatacagtg ... tttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTA




















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: 43 (upstream exon), 48 (downstream exon)
Score: 52

TGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAGgtatacagtg ... tttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 13

TGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAGgtatacagtg ... tttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

TGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAGgtatacagtg ... tttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 100

TGAGGCATGCGGCATCACTTTTCCCAACTGCAATCATTAGCGGAAGATCTCGTGATAAGgtatacagtg ... tttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgcacaaataactcctatcagcattttgcatttttctcattgtttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG
        aaataac  putative branch site (score: 100)
                          ttttgcatttttctca  putative PPT
                                             tttctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacagtgttattgttcattgcacaaataactcctatcagcattttgcatttttctcattgtttcttttagGTTTTTGACTTTGTGAAGCTAAATGAATTGTACTACGCTGGAAGCCATGGAATGGACATAATGGGCCCTGTTAGGAAGACTACTGACTCCAATGGCGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA