RetrogeneDB ID: retro_pvam_758

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_1086:125822..126380(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ZDHHC4
• Ensembl ID: ENSPVAG00000016104
• Aliases: None
• Description: zinc finger, DHHC-type containing 4 [Source:HGNC Symbol;Acc:18471]

Sequence

>retro_pvam_758
AGAAAGGAGATGCGATCCAGCACTTGCACGTGTGTAACGGGTGTGTGCACCATTTGGACCATCACTGTGTTTGGGTGAAC
AACTACATCGTGGCCTGGAATGCCAAATACTTCCTCCTCTACTTCCTGACGTTAATGGCCTCAGCTGCCACCGTGGCCAC
TACGAGCACTGTGTTTCTGGTCCAGTTGGTGGTGTGGTTGAACTTGTACCTGGAGACTTACGTTAATGACCTGGGACACT
TCCAGGTTATTGACACCATCTTTCTTATTCAGCACCTGTTCCTGACCTTCCCAAGGACTGTCTTCCTCCTGGGCCTTGTC
CTGGTGCTGAGCTGCCTCCCGAGTGGATACCTGTGCTTTGCTCTTTACCTGGCCACCACCAACCAGACCACTGACCAGTG
GTACAGAGGTGACCAGGCCTAGTGCCAGTGTTGCTCCCACGTGGCCTGGCCCCCATCAGCAGAGCCCAAGTCACGGGAAT
ATTCACTCCCTTGGGCTTTGGAGCAATCTTAGAGAGATCATTCTACCTGCAGCTGCACATTATGAGAGAAAGAAGAAA

Alignment

ORF - retro_pvam_758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 54.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKPARSKHCS-VCNRCVHRFDHHCVWVNNCIGAWNTRYFLIYLLTLTASAATVATVTTMFLVRLVMVSDL
          RK..RS..C..VCN.CVH..DHHCVWVNN.I.AWN..YFL.Y.LTL.ASAATVAT..T.FLV.LV....L
Retrocopy RKEMRSSTCT<VCNGCVHHLDHHCVWVNNYIVAWNAKYFLLYFLTLMASAATVATTSTVFLVQLVVWLNL

Parental  NLETYVDDLGHFQVIDTVFLIQYLFLTFPRIVFMMGFVLILSFLLGGYLCFAL-MAATNQTTNEWYRGNR
          .LETYV.DLGHFQVIDT.FLIQ.LFLTFPR.VF..G.VL.LS.L..GYLCFAL..A.TNQTT..WYRG..
Retrocopy YLETYVNDLGHFQVIDTIFLIQHLFLTFPRTVFLLGLVLVLSCLPSGYLCFALYLATTNQTTDQWYRGDQ

Parental  ARCQHC-PGMVRPTSAEPWVYRNSHSHGLWSNIREIFLPAAVHYERKKK
          A.CQ.C.P....P....P....N.HS.GLWSN.REI.LPAA.HYERKKK
Retrocopy A*CQCC>PTWPGPHQQSP-SHGNIHSLGLWSNLREIILPAAAHYERKKK

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_758 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.

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009547	1 retrocopy	retro_btau_643,
Dasypus novemcinctus	ENSDNOG00000009165	1 retrocopy	retro_dnov_2610,
Homo sapiens	ENSG00000136247	1 retrocopy	retro_hsap_1193,
Macaca mulatta	ENSMMUG00000015545	1 retrocopy	retro_mmul_1283,
Nomascus leucogenys	ENSNLEG00000015607	1 retrocopy	retro_nleu_2081,
Pongo abelii	ENSPPYG00000017352	1 retrocopy	retro_pabe_993,
Pan troglodytes	ENSPTRG00000018915	1 retrocopy	retro_ptro_3038,
Pteropus vampyrus	ENSPVAG00000016104	2 retrocopies	retro_pvam_1175, retro_pvam_758 ,
Ictidomys tridecemlineatus	ENSSTOG00000011605	1 retrocopy	retro_itri_1054,
Tursiops truncatus	ENSTTRG00000005001	1 retrocopy	retro_ttru_179,
Vicugna pacos	ENSVPAG00000011480	1 retrocopy	retro_vpac_177,