RetrogeneDB ID: retro_pvam_1206

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_4141:108257..108836(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF167
• Ensembl ID: ENSPVAG00000003781
• Aliases: None
• Description: ring finger protein 167 [Source:HGNC Symbol;Acc:24544]

Sequence

>retro_pvam_1206
AGGAGCTCCGAGTACCTGCGTGCCCTCTTCCTCTACCACAAGGGGGCTCAGGTGCTCCTGCTCCCAGACAACAGCTTCAT
CTTGATCTATTACTGCCTCATCCCTTTCACAGGGATTGTGGGACTACTAATCTTGACTGGAGCGGTGATGTTACTTCGTT
GTATCCAGCACCAGAAACAGCTCCAGCGAAATCGACTGACCCAACAGCAACTGAAACTGATTCCTACACATGACTATCAG
AAGGGAGATCAGTATGACGTCTGTGTCATCTGCCTGGACGAATATGAAGATGGGGACAAGCTAAGGGTACTTCCCTGTAC
TCATGCCTATCACAGCCGCTGTGTAGACCCTTGGCTCACTCGGACCCGGAAGACCTGTCCCATCTGCAAAGAGCCCGTTC
AGCAGGAGGAAGAAACTCGGGGGCAAGAAAGAGAGCCAAGGGGCCACGCTGCCTCAGAACGGACCCCTCTTCTGGGCGCC
GGCCCCAGGCTTCCCACATCCTTTGGCTCCCTAGCCCCCGCTCCGCTTGTTTTTCCTTCAACGGATCCCTCGCCCTCTCT
ATCCTCCTCTTCTTCAGCT

Alignment

ORF - retro_pvam_1206 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.98 %
• Parental protein coverage: 55.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RSSEYLRALFVYEKGARVLLVPDNSFPLGYY-LIPFTGIVGLLVLAMGAVMIVRCIQHRKRLQRNRLTKE
          RSSEYLRALF.Y.KGA.VLL.PDNSF.L.YY.LIPFTGIVGLL.L..GAVM..RCIQH.K.LQRNRLT..
Retrocopy RSSEYLRALFLYHKGAQVLLLPDNSFILIYYCLIPFTGIVGLLILT-GAVMLLRCIQHQKQLQRNRLTQQ

Parental  QLKQIPTHDYQKGDQYDVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPVHRGPGD
          QLK.IPTHDYQKGDQYDVC.ICLDEYEDGDKLRVLPC.HAYHSRCVDPWLT.TRKTCPICK.PV......
Retrocopy QLKLIPTHDYQKGDQYDVCVICLDEYEDGDKLRVLPCTHAYHSRCVDPWLTRTRKTCPICKEPVQQEEET

Parental  EEQEETPGQDGDEEEEPRDHPASEQTPLLGSSPRGPTSFGSLAPAPLIFPGSSA
          ..QE..P......E..P............GS....P..F.S..P.P.....SSA
Retrocopy RGQEREPRGHAASERTPLLGAGPRLPTSFGSLAPAPLVFPSTDPSPSLSSSSSA

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_1206 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43,
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84,
Dipodomys ordii	ENSDORG00000011757	2 retrocopies	retro_dord_277, retro_dord_432,
Equus caballus	ENSECAG00000021567	1 retrocopy	retro_ecab_583,
Felis catus	ENSFCAG00000011173	1 retrocopy	retro_fcat_99,
Mustela putorius furo	ENSMPUG00000010940	1 retrocopy	retro_mputfur_95,
Pteropus vampyrus	ENSPVAG00000003781	1 retrocopy	retro_pvam_1206 ,
Sorex araneus	ENSSARG00000011216	1 retrocopy	retro_sara_517,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,