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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatttatccaatatgttactcatattgctgcaggaaagtgagaaatagactctattccttgtgctattggacggatggcattcctatccctata...

Basic information

species Zea mays
transcript GRMZM2G412888_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412888_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g41730.1 (Oryza sativa), 5'ss of exon 5
AGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatttatccaatatgtta----ctcatattgctgcaggaaagtgagaaatagac-tctattccttgtgctattggacggatggcattcctatccctata
|| ||||||||| || || |||||| ||||||||||| | ||||| ||||| ||||||||||||||||||||||| ||||| ||||||||||||| ||||||| |||   ||   ||| |  |     ||||| || |||||  ||||| ||  |    | ||| |||  | |||||||||| ||||| |  |  |||||     
AGTTCAGAGGAAGGATATTGACACATCCAGGATAGTTGTTTTTGGGAGATCGTTAGGAGGTGCTGTTGGAGCAGTGCTTGCGAAAAACAATCCTGGCAAGgtactcatgataggaaatcttgtgtactctcatgtttctgcataaaagttagggaggcccctctgttctctctgctattggatggatgacgctagtatcc-----
















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|26557244|gb|CA829479.1|CA829479
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GNGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGG
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGG
EST: gi|71425140|gb|DR806559.1|DR806559
EST:     TTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGATCA-G                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGC
genomic: TTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGA-CAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGC
EST: gi|76018058|gb|DT945228.1|DT945228
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACCAG                         GTGGCCACTCTAATACTGGAAAATACATTTTACATCCCTACTGGATATGGC
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTT-ACATCCATACTGGATATGGC
EST: gi|71430933|gb|DR811983.1|DR811983
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTG
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTG
EST: gi|32793966|gb|CD946202.1|CD946202
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|71427907|gb|DR808957.1|DR808957
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|29129758|gb|CB380462.1|CB380462
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGNT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|149008856|gb|EE041069.2|EE041069
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACT
EST: gi|71425139|gb|DR806558.1|DR806558
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|71448310|gb|DR829360.1|DR829360
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|89253014|gb|DY624800.1|DY624800
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|148933213|gb|EC876864.2|EC876864
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|148939301|gb|EC883808.2|EC883808
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|31664225|gb|CD572950.1|CD572950
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|30705302|gb|CD058738.1|CD058738
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|76293689|gb|DV033257.1|DV033257
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|89252853|gb|DY624639.1|DY624639
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|211038058|gb|FL324597.1|FL324597
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|67011215|gb|CO439964.1|CO439964
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAANACAATCCTGACAAG                         GTGGCCACTCTAATACTGGGAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|8103365|gb|AW928006.1|AW928006
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|91055111|gb|EB165529.1|EB165529
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|67041292|gb|CO467547.1|CO467547
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|29576736|gb|CB616848.1|CB616848
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|148947394|gb|EC892802.2|EC892802
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|149014757|gb|EE044444.2|EE044444
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCT
EST: gi|71437275|gb|DR818325.1|DR818325
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAA
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAA
EST: gi|148933571|gb|EC877438.2|EC877438
EST:     CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCCAAAACAATCCTGACAAG                         GTGGCCACTCTAATACTGGAAA-TACATTTACAT
genomic: CTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACAT

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), 45 (downstream exon)
Score: 264

AGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCTGGTATTATGCTTCCCTTCTTAAGATGGTTCATAGGCGGGAGCTCTTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 218

AGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCTGGTATTATGCTTCCCTTCTTAAGATGGTTCATAGGCGGGAGCTCTTCTA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 288

AGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCTGGTATTATGCTTCCCTTCTTAAGATGGTTCATAGGCGGGAGCTCTTCTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

AGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatt ... cgtgttgcagGTGGCCACTCTAATACTGGAAAATACATTTACATCCATACTGGATATGGCTGGTATTATGCTTCCCTTCTTAAGATGGTTCATAGGCGGGAGCTCTTCTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTCAGAGGAATGACATCGACACAACCAGGATAGTTATCTTTGGAAGATCTTTAGGAGGTGCTGTTGGAGCAGTTCTTGCCAAAAACAATCCTGACAAGgtaatcaatttatccaatatgttactcatattgctgcaggaaagtgagaaatagactctattccttgtgctattggacggatggcattcctatccctata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaata