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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatatgcatgcactttttcacatgtagttgttcggtacctaactttagtatataactttctgtttgcaaaggctgaaatttccttgttcccgttttcag

Basic information

species Zea mays
transcript GRMZM2G027851_T03
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os07g47100.3 (Oryza sativa), 5'ss of exon 11
ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatatgcatgcactttttcacatgtagttgttcggtacctaactttagtatataactttctgtttgcaaaggctgaaatttccttgttcccgttttcag
| || ||||| ||| |||||||||| ||||||||||||||||||||||||||||||||||||||  | || || || || ||||||||||||||||||||||    |||    | | | |    |  |    ||  | | ||   |   | |  || | ||||    ||  ||   || |                        
ACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGACAGgtctg-atacatgttctcatacctaattcctatttatggatatggagactca--attttacttctctttcccattcgcag------------------------

upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 8
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 5'ss of exon 7
ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatatgcatgcactttttcacatgtagttgttcggtacctaactttagtatataactttct---gtttgcaaaggctgaaatttccttgttcccgttttcag
||||||||||||||||||| ||  |||||||||||||| | ||||| || ||||| ||||||||  | ||||| ||||| |||   || |  ||||||||||      |  || | |       | |  |   | || | |   |  || || || ||||  ||||   |||| ||  |  ||   ||     |             
ATGCCTTTGCTACTTTGTCGTTTCTCGCTGAGACTTTTATTTTCCTCTACGTTGGAATGGATGCATTGGACATAGAGAAATGGAGATTCGTGAGTGACAGgtatggtcactca-gtagaaacataaac-tctctttttgttcattggctata-tacataatcttcttatgtttccattgtttggttttggacag-------------

upper sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 8
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 5'ss of exon 10
ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttc-atatatgcatgcactttttcacatgtagttgttcggtacctaactttagtatataactttctgtttgcaaaggctgaaat-ttccttgttcccgttttcag
|| | ||||| || || || ||  |  |||||| |||| |||||||||||||||| || |||||| | ||||| |||||||||  | |||  ||  ||||||   || | |  ||  || |  | | |   | |   ||   ||  | |||    || ||  | ||| | |  || || ||| |  ||       |     ||   
ATACTTTTGCAACGTTATCTTTTGTTTCTGAGATTTTTATCTTCCTGTATGTTGGTATTGATGCCTTGGACATTGAGAAGTGGCGGGTTGTAAGCAACAGgtaagatttctaaatctacataattata---attcagtccaaactcatcttcctaatgtatatgtctttatataatggttgacacatttaccacccttaactt---

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|50333104|gb|CO528230.1|CO528230
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|89755588|gb|DY685957.1|DY685957
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71437105|gb|DR818155.1|DR818155
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|74238598|gb|DT646512.1|DT646512
EST:     GTGGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|78093452|gb|DV521826.1|DV521826
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71760181|gb|DR958118.1|DR958118
EST:     GTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71761590|gb|DR959527.1|DR959527
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|88750196|gb|DY534337.1|DY534337
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71446906|gb|DR827956.1|DR827956
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71758416|gb|DR956353.1|DR956353
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|78074782|gb|DV503216.1|DV503216
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|93281414|gb|EB673678.1|EB673678
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|76013009|gb|DT940179.1|DT940179
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|76293702|gb|DV033270.1|DV033270
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|74239374|gb|DT647288.1|DT647288
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71427238|gb|DR808288.1|DR808288
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|78115472|gb|DV533860.1|DV533860
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71760562|gb|DR958499.1|DR958499
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|76936699|gb|DV174843.1|DV174843
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|71440636|gb|DR821686.1|DR821686
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
EST: gi|78080129|gb|DV508541.1|DV508541
EST:     GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAG                         CCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT
genomic: GTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGT

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 7 RNA-Seq libraries.


Block sizes: 35 (upstream exon), 15 (downstream exon)
Score: 1

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACA


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

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACA


Block sizes: 48 (upstream exon), 35 (downstream exon)
Score: 12

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACA


Block sizes: 39 (upstream exon), 11 (downstream exon)
Score: 1

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACA


Block sizes: 46 (upstream exon), 28 (downstream exon)
Score: 3

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACA


Block sizes: 47 (upstream exon), 15 (downstream exon)
Score: 6

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACA


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 26

ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatat ... ccgttttcagCCCCGGTAAATCCATCGGCATAAGCTCGATTTTGCTAGGGTTGGTTCTGGTGGGGAGAGCTGCATTTGTTTTCCCATTGTCGTTTTTGTCCAACCTGACA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCTTTGCTACTTTGTCCTTCATCGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCCCTCGACATCGAGAAGTGGGAGTTTGCCAGTGACAGgttcatatatgcatgcactttttcacatgtagttgttcggtacctaactttagtatataactttctgtttgcaaaggctgaaatttccttgttcccgttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT