RetrogeneDB ID: retro_pvam_1485

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_9892:35150..36326(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPVAG00000012053
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: KLHL13
• Ensembl ID: ENSPVAG00000015989
• Aliases: None
• Description: kelch-like family member 13 [Source:HGNC Symbol;Acc:22931]

Sequence

>retro_pvam_1485
AAAACTCCCTTTGAACGACTGCCATTGTGCTTTCAGTAATAGTTTAAGCACTGTACTGAACTTGAGCTCTTCAAGGCTGC
CTGTCGCTGGCTAAGGTTAGAAGACCCTCGGATGGATTATGCTGCAAAATTAATGAAGAATATTCGTTTTCCACTGATGA
CACCACAGGACCTCATTAATTACGTGCAGACGGTAGATTTCATGAGAACAGACAATACCTGTGTGAATTTGCTTTTGGAA
GCTAGCAATTACCAAATGATGCCATACATGCAGCCGGTGATGCAGTCAGATAGAACTGCCATTCGATCGGACTCAACACA
TTTGGTTACATTAGGAGGAGTTTTGAGGCAGCAGCTGGTTGTCAGTAAAGAATTAAGGATGTATGATGAAAGGGCACAAG
AGTGGAGATCTTTAGCCCCCATGGATGCTCCGCGGTACCAGCATGGCATTGCTGTCATTGGAAACTTTCTTTATGTGGTT
GGTGGTCAAAGTAATTATGATACGAAAGGAAAAACTGCTGTCGATACAGTTTTCAGATTTGATCCTCGGTATAATAAATG
GATGCAGGTTGCATCATTAAATGAGAAGCGTACTTTCTTCCACTTGAGTGCCCTCAAAGGACATTTGTATGCTGTTGGTG
GGCGAAGTGCAGCTGGTGAACTGGCCACAGTAGAATGTTACAATCCAAGAATGAATGAGTGGAGCTATGTTGCAAAAATG
AGTGAACCCCACTATGGCCATGCTGGAACAGTGTATGGAGGCTTAATGTATATTTCAGGAGGAATTACACACGATACTTT
CCAAAATGAGCTCATGTGTTTTGACCCAGATACAGACAAATGGACGCAGAAGGCTCCAATGACTACAGTCAGAGGTTTGC
ATTGCATGTGTACAGTTGGAGACAAGCTCTATGTCATTGGTGGCAATCACTTCAGAGGAACAAGTGATTATGATGATGTT
CTAAGCTGTGAATACTATTCACCAACCCTTGACCAGTGGACACCAATTGCTGCTATGTTAAGAGGTCAGAGTGATGTTGG
AGTTGCTGTCTTTGAAAATAAAATCTATGTTGTAGGTGGATATTCTTGGAATAATCGTTGTATGGTAGAAATTGTCCAGA
AATATGACCCAGAAAAGGATGAGTGGCATAAAGTTTTTGACCTTCCAGAGTCACTT

Alignment

ORF - retro_pvam_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.18 %
• Parental protein coverage: 60.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KLPFERL-AFVLS-SNSL-KHCTELELFKATCRWLRLEEPRMDFAAKLMKNIRFPLMTPQELINYVQTVD
          K.PFERL.A.VLS.SNSL.KHCTELELFKA.CRWLRLE.PRMD.AAKLMKNIRFPLMTPQ.LINYVQTVD
Retrocopy KTPFERL<AIVLS<SNSL<KHCTELELFKAACRWLRLEDPRMDYAAKLMKNIRFPLMTPQDLINYVQTVD

Parental  FMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDTTHLVTLGGVLRQQLVVSKELRMYDEKAHEWK
          FMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSD.THLVTLGGVLRQQLVVSKELRMYDE.A.EW.
Retrocopy FMRTDNTCVNLLLEASNYQMMPYMQPVMQSDRTAIRSDSTHLVTLGGVLRQQLVVSKELRMYDERAQEWR

Parental  SLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALK
          SLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALK
Retrocopy SLAPMDAPRYQHGIAVIGNFLYVVGGQSNYDTKGKTAVDTVFRFDPRYNKWMQVASLNEKRTFFHLSALK

Parental  GYLYAVGGRNAAGELPTVECYNPRTNEWTYVAKMNEPHYGHAGTVYGGVMYISGGITHDTFQKELMCFDP
          G.LYAVGGR.AAGEL.TVECYNPR.NEW.YVAKM.EPHYGHAGTVYGG.MYISGGITHDTFQ.ELMCFDP
Retrocopy GHLYAVGGRSAAGELATVECYNPRMNEWSYVAKMSEPHYGHAGTVYGGLMYISGGITHDTFQNELMCFDP

Parental  DTDKWIQK-PMTTVRGLHCMCTVGERLYVIGGNHFRGTSDYDDVLSCEYYSPILDQWTPIAAMLRGQSDV
          DTDKW.QK.PMTTVRGLHCMCTVG..LYVIGGNHFRGTSDYDDVLSCEYYSP.LDQWTPIAAMLRGQSDV
Retrocopy DTDKWTQKAPMTTVRGLHCMCTVGDKLYVIGGNHFRGTSDYDDVLSCEYYSPTLDQWTPIAAMLRGQSDV

Parental  GVAVFENKIYVVGGYSWNNRCMVEIVQKYDPDKDEWHKVFDLPESL
          GVAVFENKIYVVGGYSWNNRCMVEIVQKYDP.KDEWHKVFDLPESL
Retrocopy GVAVFENKIYVVGGYSWNNRCMVEIVQKYDPEKDEWHKVFDLPESL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_1485 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002447	1 retrocopy	retro_cjac_3406,
Cavia porcellus	ENSCPOG00000011268	1 retrocopy	retro_cpor_590,
Loxodonta africana	ENSLAFG00000008122	1 retrocopy	retro_lafr_1018,
Macaca mulatta	ENSMMUG00000002293	1 retrocopy	retro_mmul_42,
Mus musculus	ENSMUSG00000036782	1 retrocopy	retro_mmus_121,
Nomascus leucogenys	ENSNLEG00000014736	1 retrocopy	retro_nleu_1031,
Oryctolagus cuniculus	ENSOCUG00000001993	1 retrocopy	retro_ocun_254,
Pongo abelii	ENSPPYG00000020658	1 retrocopy	retro_pabe_60,
Pteropus vampyrus	ENSPVAG00000015989	1 retrocopy	retro_pvam_1485 ,
Rattus norvegicus	ENSRNOG00000014029	1 retrocopy	retro_rnor_154,
Sus scrofa	ENSSSCG00000012637	1 retrocopy	retro_sscr_51,
Ictidomys tridecemlineatus	ENSSTOG00000012035	1 retrocopy	retro_itri_124,
Tarsius syrichta	ENSTSYG00000002521	1 retrocopy	retro_tsyr_19,