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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatcctttgtgtgctggttattgcgaacaaagaatggtttctgtaaaagattgttacagagctagtcttctcaacttccatacatgtttcttgt...

Basic information

species Zea mays
transcript GRMZM2G458208_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458208_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 5'ss of exon 4
ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatcctttgtgtgctggttattgcgaacaaagaatggtttctgtaaaagattgttacag-agcta-gtcttctcaac--ttccatacatgtttcttgt
||||| || ||||||||||| || ||||||||||| ||||||||||||||||||||||| || |||||||||||||| || ||||| |||||||| ||||||||| |     ||||    |   | ||| ||| |     |  ||    ||  |   |   ||    | ||  | || | |||  ||||| ||   | || |  
ACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAGTCAAGAATGTTGGTGCAAGCCTTGTAAAGCAGGTTGCTAATGCGACCAATGATACTGCTGGAGATGgtatggctgtacttgtaccatt-ctgttgagaatacttggtccttctgttagcattctacaactttggttatatattataaacaattccagac-catctcat--

upper sequence: GRMZM2G458208_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G33910.1 (Glycine max), 5'ss of exon 4
ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatcctttgtgtgctggttattgcgaacaaagaatggtttctgtaaaagattgttacagagctagtcttctcaacttccatacatgtttcttgt
|| || || |||||||||||||| ||||| | ||| |||||| | ||||| || ||||| || |||||||||||||| |||||||||   ||||| ||||||| |  ||  | |   | ||||  |||       |  ||   | |     |  |  |  |       || |  |      | | ||  |  ||    | 
ACCGTTGCTAAGAGCATTGAATTCAAGGACAAAGTCAAGAATATCGGTGCCAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGACGTGGCTGGTGATGgtaagctattatatccatactgg--attatactttattaa--atcttcagcattggctactttgttattaataatga-gggtacaatctaatttggcag-

upper sequence: GRMZM2G458208_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G25630.1 (Glycine max), 5'ss of exon 4
ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgac-atcctttgtgtgctggttattgcgaacaaagaatggtttctgtaaaagattgttacagagctagtcttctcaacttccatacatgtttcttgt-
||||| ||||||||||||||||| ||||||| ||| |||||||||||||| || ||||| || |||||||| ||||| ||||||||    ||||| ||||||| |   ||   |     |  | || |    || |   ||   ||||| ||  || ||  |      || ||    |          |  || || ||   
ACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGAATGTTGGTGCCAGTCTTGTAAAGCAGGTTGCAAATGCTACTAATGATGTGGCTGGTGATGgtaagctgatatatccaaagaagattgtgcttaatagtcaact-tttctctattag-ttactttgttacttgtacaatactagattgcatgtggttgttaaa

upper sequence: GRMZM2G458208_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G19980.1 (Glycine max), 5'ss of exon 4
ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatcctttgtgtgctggttattgcgaacaaagaatggtttctgtaaaagattgttacagagctagtcttctcaacttccat-acatgtttc--ttgt-
||||| ||||||||||||||||| ||||||| ||| |||||||||||||| || ||||| || |||||||||||||| ||||||||    ||||| ||||||| |      | | |     |   ||||      |       ||| |||  |   | |||||   | || |  |   |  ||  ||  |||| |||  | || 
ACTGTTGCAAAGAGCATTGAATTCAAGGATAAAGTTAAGAATGTTGGTGCCAGTCTTGTAAAGCAGGTTGCTAATGCTACTAATGATGTGGCTGGTGATGgtaagctga--tatatccaaagaagattgtacttcatagtaaatttttgtctat--tggttacttcgttacttgtacaatattagattgcatggttccgtggtt

upper sequence: GRMZM2G458208_T01 (Zea mays), 5'ss of exon 3
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 5'ss of exon 4
ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatcctttgtgtgctggttattgcgaacaaagaatggtttctgtaaaagattgtta----cagagctagtcttctcaacttccatacatgtttcttgt-----------------------
||||| || ||||||||||| || ||||||||| | ||||| |||||||| || |||||||||||||||||||| || || ||||||   ||||| |||||||     | |  | |     | |||   ||         |  || ||  |   | ||||||    |  | ||| || | | ||      |   ||| |||                          
ACTGTTGCCAAGAGCATTGAGTTCAAGGATAGAATTAAGAACGTTGGTGCCAGTCTTGTGAAACAGGTTGCTAACGCCACAAATGACGTAGCTGGTGATGgta-agtgttccctttcaatggattaaaacgttttttctgtttttgcta-attgggttgttagtctcctatctactcatattaatcggtgtttttgtatctgacaaaatatatggtatgcgttacag

upper sequence: GRMZM2G458208_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 5'ss of exon 4
ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatcctttgtgtgctggttattgcgaacaa-agaatggtttctgtaaaagattgttacagagctagtcttctcaacttccatacatgtttc--ttgt---
||||| ||||| |||||||| || |||||| || | ||||||||||||||||||||||||||||||||||| ||||| ||||||||    || || ||||||| |   || | |||       ||| ||     |  | ||||||||      ||||||  ||    | || |     || ||||   | ||| ||   | ||   
ACTGTTGCAAAAAGCATTGAGTTCAAGGATCGAATCAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCAAATGCCACTAATGATGTAGCAGGAGATGgtaagttttcatctgttgcaactttagtggttctattaaaatggttt-----gaagatt-ctattttgataattgatgcatcttctgcaaatgatttaatggttaa

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|31355867|gb|CD440224.1|CD440224
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GCACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|61119163|gb|DN560124.1|DN560124
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|13388799|gb|BG462407.1|BG462407
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTG-TTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|31361464|gb|CD445821.1|CD445821
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|89754394|gb|DY685176.1|DY685176
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGGTGC
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGG-TGC
EST: gi|88747169|gb|DY531310.1|DY531310
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|31441079|gb|CD510510.1|CD510510
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|31349389|gb|CD433746.1|CD433746
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|94476466|gb|EB705424.1|EB705424
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
EST: gi|31355665|gb|CD440022.1|CD440022
EST:     AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATG                         GTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA
genomic: AAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCA

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: 519

ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 303

ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 296

ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 322

ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatc ... aaaatttcagGTACCACATGTGCCACTGTTTTGACAAAAGCAATATTTACTGAGGGGTGCAAATCTGTTGCGGCTGGAATGAATGCAATGGATTTAAGGCGCGGAATCTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGTAGCAAAGAGCATTGAATTTAAGGATAGAGTAAAGAATGTTGGTGCAAGCCTTGTGAAACAGGTTGCTAATGCAACTAATGACACTGCTGGCGATGgtatgacatcctttgtgtgctggttattgcgaacaaagaatggtttctgtaaaagattgttacagagctagtcttctcaacttccatacatgtttcttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acaaagaa