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

gtttgccactttgtctcctatatttcatataatattcatatctgtctactagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA

Basic information

species Zea mays
transcript GRMZM2G017835_T02
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017835_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA10G44050.1 (Glycine max), 3'ss of exon 8
--------------gtttgccactttgtctcctatatttcatataatattcatatctgtctactagttatgacattagttctatgtccaaacttctctcttgcct-tcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA-----------------
                   || | || |||  | | || |   |  || |  | | | | || ||||| |        |  | | || |   |  |   |  ||| |  | || ||||||||| ||  ||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||| | || || ||||| || |                 
gttttcttcccccccaccccctccttttcttttcttttcccccttgtagttctctttttttaatagttttcttgcatatggt-tatcaatgttcttgagtctcctctttttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTCTTCCTCCAT

upper sequence: GRMZM2G017835_T02 (Zea mays), 3'ss of exon 7
lower sequence: GLYMA20G38770.1 (Glycine max), 3'ss of exon 8
----gtttgccactttgtctcctatatttcatataatattcatatctg---tctactagttatgacattagttctatgtccaaacttctc---tcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA-----------------
      || || |  |  | ||    |||| | |  | |||   |      |||  |  || | |   |  |  | |   |||  ||||     |||  |||  | || ||||||||| ||  ||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||| | || || ||||| || |                 
gtattcttccccccctccccccctcttttcttttcttcttccccttgcagttctcttctttttaatggttttcttgttatcaatgttcttgaaccttatcttt-ttatgtagAGGAACTGTTCGATATGCTAGTGTTCATGCTCATTTGGGGAGAACTGCTAGTAGAAGAGATGATCTTGAATCTCTTGCATACACACTAGTATTCCTTCAT

upper sequence: GRMZM2G017835_T02 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0004g01090.t01 (Vitis vinifera), 3'ss of exon 8
gtttgccactttgtctcctatatttcatataatattcat-atctgtctactagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA-----------------
    |  | ||  | |  | | | |     |   ||  | || | |  |||  || |         |  ||     |   | | |  ||  | | | ||| || ||||| || |||||||||||||| ||||| || || |||||||| || ||||| ||||| ||| | ||||| ||||| ||||                 
----gtgaattgatgttgtgtttgtgggccatgctttgtgatttttgaacttattttttttaatccttcattcttgattatttttactgtttgcttcatccagGGGAACTGTGAGATATGCTAGTGTTCATGCTCACTTGGGAAGAACTGCCAGCAGAAGAGACGATCTAGAGTCTCTTGCATATACACTCATCTTCCTTCAT

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|32835900|gb|CD975578.1|CD975578
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|22819487|gb|BU499577.1|BU499577
EST:     ACTGCTAATGGGCAGCATGTTAGCTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATAATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTA
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATA-TGCTAGTGTCCATGCACATTTAGGAAGAACCGCTA
EST: gi|26559748|gb|CA831983.1|CA831983
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|148988749|gb|EE031658.2|EE031658
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|31355100|gb|CD439457.1|CD439457
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|60345255|gb|DN212228.1|DN212228
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|32835164|gb|CD974842.1|CD974842
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
EST: gi|31440950|gb|CD510381.1|CD510381
EST:     ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAG                         AGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG
genomic: ACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAG

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: 295

CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 216

CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 210

CAACAAAGTGGAGAGATACTGCTAATGGGCAGCATGTTAGTTATGATCAACGTCCTGATGCCTTTAGgtttgccact ... cataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA
                              cttctctcttgccttc  CT-rich tract
                                           ttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgccactttgtctcctatatttcatataatattcatatctgtctactagttatgacattagttctatgtccaaacttctctcttgccttcataatctagAGGAACAGTCAGATATGCTAGTGTCCATGCACATTTAGGAAGAACCGCTAGCAGGAGAGATGATTTGGAGTCACTTGCCTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG