RetrogeneDB ID: retro_amel_664

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192557.1:564225..564760(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NMRK1
• Ensembl ID: ENSAMEG00000005312
• Aliases: None
• Description: nicotinamide riboside kinase 1 [Source:HGNC Symbol;Acc:26057]

Sequence

>retro_amel_664
AAGACAACACTGGCTAAGAATTTGCAGAAATACCTTCCAATCTGCAGCATCATATCTCAGGATGATTTCTTTAAGCCAGA
GTCTGAGATAGAGAAAAATACAGATGGATTTCTGCAGTATGACGTGCTTGAAGCACTTAACATGGAAAAAATGATACCCA
CCATTTCCTGCTGGATGAAAAGCCCAAGATAATCACTGTTAACAACAGACTCTGGAAATGCTGAGAAATTTCCATATAAA
TCATTGAAAGCTTCCTTCTCTTTAACTATAAGCCCCTTGACACTCTATGGAACAGAAGCTACTTTCTGACCATTCCATAC
AAAGAATGTAAAAGGAGAAAGAGTATAAAGATCTACGAGCCCCCAGACCCCCCAGGGTACTTTGATGGCCACATGTGGCC
CATGCATCCAAAGCACAGACAAGAAATGGAGACATCAGGTGGAAAACTGTTTACCTAAACAGAACAAAATCTGAAGAGGA
CCTCTTCTCACAAGTGTATGAAGATCTAATACAGAAACTAGCAAAGCAGAAGTGT

Alignment

ORF - retro_amel_664 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.8 %
• Parental protein coverage: 89.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KTTLAKNLQKHLPNCSVISQDDFFKPKSEIEIDTNGFLQYDVLEALNMEKMMSAISCWMESPRHSLVSTH
          KTTLAKNLQK.LP.CS.ISQDDFFKP.SEIE..T.GFLQYDVLEALNMEKM...ISCWM.SPR.SL..T.
Retrocopy KTTLAKNLQKYLPICSIISQDDFFKPESEIEKNTDGFLQYDVLEALNMEKMIPTISCWMKSPR*SLLTTD

Parental  RGSSEEIP-ILIVEGFLLFNYKPLDTLWNRSYFLTIPYEECKRRRSTRVYEPPDVPGYFDGHVWPMYLKH
          .G..E..P.I.I.E.FLLFNYKPLDTLWNRSYFLTIPY.ECKRR.S...YEPPD.PGYFDGH.WPM..KH
Retrocopy SGNAEKFP<I*IIESFLLFNYKPLDTLWNRSYFLTIPYKECKRRKSIKIYEPPDPPGYFDGHMWPMHPKH

Parental  RQEVE-NITWEIVYLDGTKSEEDLFSQVYEDLIQELAKQKC
          RQE.E..I.W..VYL..TKSEEDLFSQVYEDLIQ.LAKQKC
Retrocopy RQEME<DIRWKTVYLNRTKSEEDLFSQVYEDLIQKLAKQKC

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_664 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_664 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005312	1 retrocopy	retro_amel_664 ,
Felis catus	ENSFCAG00000028823	1 retrocopy	retro_fcat_1087,
Macropus eugenii	ENSMEUG00000009787	1 retrocopy	retro_meug_275,
Mustela putorius furo	ENSMPUG00000012337	1 retrocopy	retro_mputfur_634,
Pteropus vampyrus	ENSPVAG00000006121	1 retrocopy	retro_pvam_293,
Tupaia belangeri	ENSTBEG00000004063	2 retrocopies	retro_tbel_1021, retro_tbel_4275,
Tarsius syrichta	ENSTSYG00000004232	1 retrocopy	retro_tsyr_718,