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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttcttgttcttccattgtaaaactttaccattaccttctttgccaatacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC

Basic information

species Zea mays
transcript GRMZM2G058584_T01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 9
gtttgttcttgttcttccattgtaaaactttaccattaccttctttgccaatacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC
                            | ||   | | | | | ||  ||   ||| |    |   |      |  |  |  |  |  || || ||| |  ||||||||||||||| ||||| |||||||||||||||||||||||||| ||||| ||||| || || |||||||| || |||||||||||||||||||||||| 
--------------------------gttctattctgatcat-tctgtaaa---atcctgaacaatatctgccctggtgacaatattt-ttcttgtttgatggcagAACAGTGAAGCCATGGTTTCTATAGACATGCCTGCTGGCCCTTCAGAAGTATTAGTGATAGCGGATAAATATGCAAACCCAGTTCATGTTGCTGCTGATT

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA08G08630.1 (Glycine max), 3'ss of exon 8
gtttgttcttgttcttccattgtaaaactttaccattaccttctttgccaatacatctttt-ctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC
||  | | |   |||  |  | |  |  ||   ||||   || |    |   | ||||| |  ||| ||  ||     ||    || |  ||   | | | ||||||||||||||||| ||||| || || |||||||| ||||| || |||||||||||||||||||| || ||  | ||||  ||   |||||| ||||||||| 
gtgagctttgaatctctctctatctattttatacattgtgtt-tcactcttcagatcttatattatagtttatcccgctttacattattgttgaaaatattctgcagAACAGTGAAGCCATGGTTTCAATTGACATGCCAGCTGGTCCATCTGAAGTTTTAGTCATTGCCGACAAGCATGCGATTCCTCGTCATGTAGCTGCTGATT

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 9
gtttgttcttgttcttccattgtaaa-actttaccattaccttc---tttgccaatacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC
                     ||||  |  ||   ||| | ||    |||    ||   | |   ||||   |  |  |||       |  ||| || | | | ||||||||||||||||| ||| | || || |||||||| ||||| || ||||||||||| |||||||| || ||  | || |  ||   |||||| || |||||| 
---------------------gtaagcatgtttatattgcattaaaatttatggatctgtatccactattacatttcattt------cttgaatcttaaatcttctgcagAACAGTGAAGCCATGATTTCAATTGACATGCCGGCTGGTCCATCTGAAGTTTTGGTCATTGCAGACAAGCATGCAATTCCTTCTCATGTAGCAGCTGATT

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 11
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 8
gtttgttcttgttcttccattgtaaaactttaccattaccttctttgccaatacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC
                  || |  |   || | || |  ||| | | | ||    | |    | |  || | |  | ||      ||  |||||   |||||||||||||| || || ||||| || || || ||||||||||| ||||| |||||  |||| ||||||||  || | || |  |||||| |  |||| || ||  
----------------gtatagatatcgttcatcaattacttttgtcctaacttgtttggagtctc-tagactactcttt--aacctgctttttcccttactgcagAACAGCGAGGCAATGGTCTCAATCGATATGCCTGCTGGTCCTTCAGAAGTCCTAGTTATTGCTGACGAACATGCTAGTCCAGTTTACATTGCAGCAGACT

upper sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 11
lower sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 11
----------gtttgttcttgttcttccattgtaaaactttaccattaccttctttgcca-atacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC
           |||  |           |||| ||  ||      || |  ||| |   | | ||||||| ||| || ||   |  | ||||  ||||  ||||||||   |  ||||| |||||||||||||| || || || |||||||| || || || |||||| |||||||||| || ||| | || || || |||||| ||||||| ||| 
gtaggcacacatttccttccaaaagattattggaactctacttttttgctgtctatatgatacacatcttatct-tgatatgattctgttgcttttctt-tttttattcatcaacagAATAGTGAAGCTATGGTTTCAATTGATATGCCTGCGGGTCCATCAGAAGTTCTAGTCATTGCCGACAAACATGCTAATCCTGTTCATATTGCTGCAGATT

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|89758985|gb|DY687956.1|DY687956
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|8516559|gb|BE123284.1|BE123284
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|21331772|gb|BQ487153.1|BQ487153
EST:     TTTTTTGACCTGGTTACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|23357617|gb|BU645266.1|BU645266
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|38688105|gb|CK145136.1|CK145136
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|71432207|gb|DR813257.1|DR813257
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|76012899|gb|DT940069.1|DT940069
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|211215840|gb|FL096753.1|FL096753
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|32840983|gb|CD980664.1|CD980664
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATACACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
EST: gi|38687960|gb|CK144991.1|CK144991
EST:     TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG                         AACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT
genomic: TTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAGgtttgttctt ... tttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC
                                ttctaat  putative branch site (score: 2)
                                      tttttatttt  CT-rich tract
                                ttctaatttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttcttgttcttccattgtaaaactttaccattaccttctttgccaatacatcttttctatggtaaattgtttttgcggttctaatttttattttactgcagAACAGTGAAGCTATGGTATCTATAGACATGCCTGCTGGCCCTTCTGAAGTTTTAGTCATTGCTGATAAATACGCGAACCCAGTTCATGTTGCTGCTGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT