RetrogeneDB ID: retro_pvam_1175

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_36713:3351..3969(+)
• 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_1175
TTCGAGTTTATAAATTCAGTGATGTTCTCAAAGAACGTGAGGTGCTCTGCTTGTGTCTTAAGGAAAGAGATGCGATCCAG
GCACTGGCACGTGTGTAACCGGTGTGTGCACCATTTGGACCATCACTGTGTTTGGGTGAACAACTACATCGTGGCCTGGA
ATGCCAAATACTTCCTCCTCTACTTCCTGACGTTAATGGCCTCAGCTGCCACCGTGGCCACTACGAGCACTGTGTTTCTG
GTCCAGTTGGTGGTGTGGTTGAACTTGTACCTGGAGACTTACGTTAATGACCTGGGACACTTCCAGGTTATTGACACCAT
CTTTCTTATTCAGCACCTGTTCCTGACCTTCCCAAGGACTGTCTTCCTGCTGGGCCTTGTCCTGGTGCTGAGCTGCCTCC
CGAGTGGATACCTGTGCTTTGCTCTTTACCTGGCCACCACCAACCAGACCACTGACCAGTGGTACAGAGGTGACCAGGCC
TAGTGCCAGTGTTGCTCCCACGTGGCCTGGCCCCCATCAGCAGAGCCCAAGTCACGGGAATATTCACTCCCTTGGGCTTT
GGAGCAATCTTAGAGAGATCATTCTACCTGCACTGCACATTATGAGAGAAAGAAGAAA

Alignment

ORF - retro_pvam_1175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.03 %
• Parental protein coverage: 59.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  YEF-DEVMFPKNMRCSTCGLRKPARSKHCSVCNRCVHRFDHHCVWVNNCIGAWNTRYFLIYLLTLTASAA
          .EF...VMF.KN.RCS.C.LRK..RS.H..VCNRCVH..DHHCVWVNN.I.AWN..YFL.Y.LTL.ASAA
Retrocopy FEFINSVMFSKNVRCSACVLRKEMRSRHWHVCNRCVHHLDHHCVWVNNYIVAWNAKYFLLYFLTLMASAA

Parental  TVATVTTMFLVRLVMVSDLNLETYVDDLGHFQVIDTVFLIQYLFLTFPRIVFMMGFVLILSFLLGGYLCF
          TVAT..T.FLV.LV....L.LETYV.DLGHFQVIDT.FLIQ.LFLTFPR.VF..G.VL.LS.L..GYLCF
Retrocopy TVATTSTVFLVQLVVWLNLYLETYVNDLGHFQVIDTIFLIQHLFLTFPRTVFLLGLVLVLSCLPSGYLCF

Parental  AL-MAATNQTTNEWYRGNRARCQHC-PGMVRPTSAEPWVYRNSHSHGLWSNIREIFLPA-AVHYERKKK
          AL..A.TNQTT..WYRG..A.CQ.C.P....P....P....N.HS.GLWSN.REI.LPA...HYERKKK
Retrocopy ALYLATTNQTTDQWYRGDQA*CQCC>PTWPGPHQQSP-SHGNIHSLGLWSNLREIILPA<TAHYERKKK

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_1175 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,