RetrogeneDB ID: retro_pvam_533

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_3637:432986..433535(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUDT21
• Ensembl ID: ENSPVAG00000014583
• Aliases: None
• Description: nudix (nucleoside diphosphate linked moiety X)-type motif 21 [Source:HGNC Symbol;Acc:13870]

Sequence

>retro_pvam_533
CCTCTCACCAACTATACTTTTGGTACAAAAGAGCCCCTCTATGACGACAGCTCTGTTGCAGCCAGATTTCAGCGCATGAG
GGAGGAATCTGATAAAATTGGAATGAGGAGGACTACACAAATGGTTCTGATTGTACATGAGCACCGGCTACCCCCATGTG
CTTCTGCTACAGCTGGGAACAATTTATTCAAATTACCTGGTGGTAATCCAAGAGAAGATGAAGTTGAAGGACTAAAGTGC
TTAATGATAGAGATATTGGGTCGTCAAGATGGAGTCCTGCAAGACCCGGTTCCTGATGACTGCATTGGTAACTGATGGAA
ACCAAACTTTGAACCTCCTCAGTATCCCTATATTCCTGCACATATTACAAAACCTAAGGAACATAAGAAGTTGTTTTTGG
TTCAACTTCAAGAGAAAGTCCTGTTTGTGGTTCCTAAAAATTACAACCTGGTAGCTGCACCGGTGTTTGTATGACGACAA
TGCCCCTGGTATGGACCCATCGTTTCTAGTCTCCCTCAGCTTTTGAGCAGGTTCAGTTTTACACACAAC

Alignment

ORF - retro_pvam_533 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.01 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLTNYTFGTKEPLYEKDSSVAARFQRMREEFDKIGMRRTVEGVLIVHEHRLP-HVLLLQLGTTF-FKLPG
          PLTNYTFGTKEPLY..DSSVAARFQRMREE.DKIGMRRT...VLIVHEHRLP.HVLLLQLGT...FKLPG
Retrocopy PLTNYTFGTKEPLYD-DSSVAARFQRMREESDKIGMRRTTQMVLIVHEHRLP>HVLLLQLGTIY<FKLPG

Parental  GELNPGEDEVEGLKRLMTEILGRQDGVLQDWVIDDCIGNWWRPNFEPPQYPYIPAHITKPKEHKKLFLVQ
          G..NP.EDEVEGLK.LM.EILGRQDGVLQD.V.DDCIGN.W.PNFEPPQYPYIPAHITKPKEHKKLFLVQ
Retrocopy G--NPREDEVEGLKCLMIEILGRQDGVLQDPVPDDCIGN*WKPNFEPPQYPYIPAHITKPKEHKKLFLVQ

Parental  LQEKALFAVPKNYKLVAAPLFELYDNAPGYGPIISSLPQLLSRFNFIYN
          LQEK.LF.VPKNY.LVAAP.F......P.YGPI.SSLPQLLSRF.F..N
Retrocopy LQEKVLFVVPKNYNLVAAPVF-V*RQCPWYGPIVSSLPQLLSRFSFTHN

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_533 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012724	3 retrocopies	retro_cjac_1121, retro_cjac_2211, retro_cjac_4100,
Echinops telfairi	ENSETEG00000013634	1 retrocopy	retro_etel_622,
Loxodonta africana	ENSLAFG00000028465	1 retrocopy	retro_lafr_610,
Macaca mulatta	ENSMMUG00000019906	1 retrocopy	retro_mmul_1360,
Mustela putorius furo	ENSMPUG00000003451	1 retrocopy	retro_mputfur_158,
Oryctolagus cuniculus	ENSOCUG00000017224	2 retrocopies	retro_ocun_154, retro_ocun_87,
Pteropus vampyrus	ENSPVAG00000014583	2 retrocopies	retro_pvam_533 , retro_pvam_711,
Sarcophilus harrisii	ENSSHAG00000009651	1 retrocopy	retro_shar_469,
Sus scrofa	ENSSSCG00000029848	2 retrocopies	retro_sscr_117, retro_sscr_185,
Tarsius syrichta	ENSTSYG00000014602	4 retrocopies	retro_tsyr_1685, retro_tsyr_1888, retro_tsyr_790, retro_tsyr_988,