Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtcttatcctctcatacagtctcatttcattcactttgatttgtagactgtagtactatcgtttatggcttattatcagtatgaggctatgaacgt...

Basic information

species Zea mays
transcript GRMZM2G420119_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420119_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os01g38990.1 (Oryza sativa), 5'ss of exon 4
TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtcttatcctctcatacagtctcatttcattcactttgatttgtagactgtagtactatcgtttatggcttattatcag--tatgaggctatgaacgt---
||||||||| |||||  ||| | | | |||  ||| || || || |||||||| |||||||||||||||||||| |||||| |||| || ||||||||||||||||| | ||       |||    | |||  |    ||  | ||     || |||   | |   |    || ||  || |    ||    ||    |  |   
TTGGGAAATGCTGGTAGACAGCCAGCATATGGTGGTATCAAGGACGTTTTCAAAACTGTTTACAAGGAAGGAGGCGCACGAGCTTTATACCGTGGAGTAGgtacgtcctgtctg-----acaactccctttgctatggttgaagttagcatctttaggtttgttagtgtgagcgtaacataaaatcatatttcttctgatctgct

upper sequence: GRMZM2G420119_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv04s0008g01060.t01 (Vitis vinifera), 5'ss of exon 4
TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgt-cttatc--ctctcatacagtctcatttcattcactttgatttgtagactgtagtactatcgtttatggcttattatcagtatgaggctatgaacgt
 || ||| ||        || |   | ||||||||||||||||||||||| || | ||| ||||||||||| || | |||  |  ||||||| || ||||||| || ||||     | |  |||| |  || | ||    |||| ||   || ||     | ||||   |  ||| |    ||   || | |  |  |   | 
ATGAGAAGTTTGCAAGCTCAGCCTGCTTATAATGGCATAAAAGATGTTTTTAAAAGTGTCTACAAGGAAGGGGGAGTACGGGCACTGTATCGAGGTGTAGgtatgtgcttactggttattttaca-ttacaatacacaatcttttatggctatacatatatgctatttgtagtggttctgaatggata-gtgttttagtttg-
















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|78118637|gb|DV537021.1|DV537021
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|74244724|gb|DT652638.1|DT652638
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|149079552|gb|EE168537.2|EE168537
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|149013497|gb|EE042998.2|EE042998
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|74234934|gb|DT642848.1|DT642848
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|71441966|gb|DR823016.1|DR823016
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|71324252|gb|DR798826.1|DR798826
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|110941380|gb|EE161537.1|EE161537
EST:     CTAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|148937578|gb|EC881763.2|EC881763
EST:     CAAGACTGTTTTCAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|149060805|gb|EE157256.2|EE157256
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTTTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|76924684|gb|DV170083.1|DV170083
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|148930077|gb|EE286023.2|EE286023
EST:     AAGACTGTTTACAA-GAAGGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: AAGACTGTTTACAAGGAA-GGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|149027733|gb|EE154578.2|EE154578
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|149042104|gb|EE047082.2|EE047082
EST:     ATCTTTGTAT-GGGGAGTAGG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATA
genomic: ATCTTTGTATCGTGGAGTA-Ggtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATA
EST: gi|89249817|gb|DY621603.1|DY621603
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTGGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
EST: gi|67016215|gb|CO444964.1|CO444964
EST:     CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAG                         GCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT
genomic: CAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATAT

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), 48 (downstream exon)
Score: 77

TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATATATGAAGATCTGAAATCTCAAGTTCCAGACGATTACAAGGATTCTGTTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 43

TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATATATGAAGATCTGAAATCTCAAGTTCCAGACGATTACAAGGATTCTGTTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATATATGAAGATCTGAAATCTCAAGTTCCAGACGATTACAAGGATTCTGTTAT


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 50

TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtctta ... tgaatttcagGCCCAACTCTTATTGGTATTCTTCCATATGCTGGCTTGAAGTTTTACATATATGAAGATCTGAAATCTCAAGTTCCAGACGATTACAAGGATTCTGTTAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGGGAAATTCTGGTCAACAACAAACGTATAATGGCATAAAAGATGTTTTCAAGACTGTTTACAAGGAAGGAGGTGCACGATCTTTGTATCGTGGAGTAGgtacgtcttatcctctcatacagtctcatttcattcactttgatttgtagactgtagtactatcgtttatggcttattatcagtatgaggctatgaacgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG