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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagactgctcgctcttccattcttcttatgctatttatgataac...

Basic information

species Zea mays
transcript GRMZM2G097226_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 13
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttcttcgccttccatcctaggttttctattagctgttgtatacac----tgctcaagactgctcgctcttcc-attcttcttatgctatttatgataac
 |||||||| |  || |||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| |||||||| |||||||| || |||||||| ||||     ||| |||| |  |||| | ||   | ||||| |||     || | | || |  |  |||  || || | | || ||| |   |   |  |
GGAAAGCTTTGAATATCTTGATGCACCAGTTGAGAGAATTGCTGGAGCTGATGTACCCATGCCCTATGCTGCCAATCTTGAGAGGATGGCTGTCCCACAGgtccttttctgt---ttctatccaaaattttatgttgtgtcttgtacacatgttttgtttatgattcttttctccaccgatgcattttgtgccaaggac--ttgc

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA02G46380.1 (Glycine max), 5'ss of exon 13
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagac---tgctcgctcttccattcttcttatgc-tatttatgataac
 || || || |  || ||||||||||| |||||||| ||||| || |||||||| || ||||| ||||| || || || || ||||||||||| || |||||  |  |  |    |   |      ||||||| | |  |  |    |   |    ||||    |  ||  | ||    ||     |||  | | |||  | | 
GGAGAGTTTTGGTTATCTTGATGCACCGGTTGAGAGAATTGCCGGGGCTGATGTTCCCATGCCATATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgtaatgattcttaaatattaatt---gttttctgtgactttgtcagcatgatttggaagatattttttcattattttgatccagaaatgtatttctattttga-

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA14G02380.1 (Glycine max), 5'ss of exon 13
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagactgctcgctcttccattcttcttatgctatttatgataac----
 || || || |  || || |||||||| |||||||| |||||||| |||||||| || ||||| ||||| || || || || ||||||||||| || |||||  |  |  |    |   |      ||||||| |   || ||||   ||    |    |    |   |     ||| |  |  ||  || |||    |     
GGAGAGTTTTGGTTATCTAGATGCACCGGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgtaatggttcttaaatattaatt---gttttctgt-gacttttgtcagcatgatttggaagatttgttttcattattttgatcctgaaatgtatttgtattttg

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 13
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagactgctcgctcttccattcttcttatgctat-ttatgataac--
|||||| || |  || ||||||||||| |||||||| |||||||| |||||||| || ||||| ||||| || || || || ||||||||||| || |||||  |  |  |    |   |      ||||||| | |  |  |    |   |    |||| |  | |   ||   ||  ||      | | ||   ||  |  
AGAAAGTTTTGGTTATCTTGATGCACCCGTTGAGAGAATTGCTGGGGCTGATGTTCCCATGCCTTATGCAGCAAATCTGGAAAGAATGGCTGTCCCACAGgtaatgattcttaaatattaatt---gttttctgtgactttgtcagcatgatttggaagatttgttgtcattattttgatccagaaatgtatttctatttcga

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 14
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtc--------ctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagactgctcgctcttccattcttcttatgctatttatgataac
||| |||||  ||||| | |||||||| || ||||||||||| ||||||||||| || ||||| ||||| || ||||| |||||| ||||| |||| |||||         | |||||| || |   |  || ||||   | ||  ||||| |  |      |  |||      | |  | ||                         
AGAGAGCTTTTCGTACTTGGATGCACCGGTCGAGAGGATTGCAGGAGCTGATGTTCCAATGCCGTATGCAGCTAACCTAGAGAGATTGGCTCTTCCTCAGgtttgttttgtcccttctttgcatcgaaaacttggttcaattttgtctgttattaatga-atttgagatgaaatgattctgcag------------------------

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 14
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtc--ctcttcttcg--ccttccatcctaggttttctatta---gctgttgtatacactgctcaagactgctcgctcttc-cattcttcttatgctatttatgataac
 || ||||| |  || |||||||||||||| || |||||||| || |||||||| || ||||| |||||||| || || |||||||||||||| || |||||    |||| || |   |||| | | |   |||  ||| |   ||| ||||     |  ||     |   |   | |    || | | || |   |||         
GGAGAGCTTTGGTTATCTTGATGCACCAGTGGAAAGGATTGCCGGGGCTGATGTTCCCATGCCTTATGCTGCTAATCTCGAGAGAATGGCTGTCCCACAGgtagattcttttttgattcttctagcttgattttattatcataagctcttgttcttccaccttgcatccaataaatttgggtatccatgtttttagatta--------

upper sequence: GRMZM2G097226_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 13
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagact-gctcgctcttccattcttcttatgctatttatgataac
 || ||||| |  |  ||||||||||| || || |||||||| || || ||| | || ||||| ||||| || || ||||||||||||||| |||| |||||   | || |    |||   | | | ||||||  ||  |    | |||| || |  ||| | ||| |   |       ||  |   || |   ||  |  
GGAGAGCTTTGATTCTCTTGATGCACCTGTCGAAAGGATTGCAGGGGCAGATATTCCCATGCCTTATGCAGCAAATCTTGAGAGAATGGCTCTTCCACAGgtatgcatcctgatattct-cctttgtttttcttgtaattacattctacattgtttcagatttgctggtgatctggaaatttatggcctgtccttggaatt

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|89754920|gb|DY685537.1|DY685537
EST:     ATGTACCTATGCCCTATGCTGCCAACCCTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|78092463|gb|DV520837.1|DV520837
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|60394298|gb|DN227168.1|DN227168
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|31354296|gb|CD438653.1|CD438653
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|76915086|gb|DV165815.1|DV165815
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|88758101|gb|DY542242.1|DY542242
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|33097928|gb|CF057888.1|CF057888
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|88757272|gb|DY541413.1|DY541413
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|32931889|gb|CF036701.1|CF036701
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|37386471|gb|CF630421.1|CF630421
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|78121283|gb|DV539667.1|DV539667
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|76912074|gb|DV164558.1|DV164558
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|32826620|gb|CD966298.1|CD966298
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGACTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|86473456|gb|DY239826.1|DY239826
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
EST: gi|211019433|gb|FL375798.1|FL375798
EST:     ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTYCGCAG                         GTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA
genomic: ATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCA

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), 46 (downstream exon)
Score: 96

AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCAATGGCAGCAGCTGCCTGATTGGTGGACAAGCCTTTCTGTTTTCCTTCCA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 99

AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCAATGGCAGCAGCTGCCTGATTGGTGGACAAGCCTTTCTGTTTTCCTTCCA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 130

AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCAATGGCAGCAGCTGCCTGATTGGTGGACAAGCCTTTCTGTTTTCCTTCCA


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

AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttct ... ttgcttacagGTCGATGACATTGTGCGGGCGGCAAAGCGGGCCTGCTACAGGGCAGTACCAATGGCAGCAGCTGCCTGATTGGTGGACAAGCCTTTCTGTTTTCCTTCCA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAGCTTCGCGTACCTTGATGCACCAGTTGAGAGGATTGCTGGAGCTGATGTACCTATGCCCTATGCTGCCAACCTTGAGAGAATGGCTGTTCCGCAGgtcctcttcttcgccttccatcctaggttttctattagctgttgtatacactgctcaagactgctcgctcttccattcttcttatgctatttatgataac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgccttcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctcgctc