RetrogeneDB ID: retro_amel_1716

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194068.1:256929..257216(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000011483
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NAA38
• Ensembl ID: ENSAMEG00000001162
• Aliases: None
• Description: N(alpha)-acetyltransferase 38, NatC auxiliary subunit [Source:HGNC Symbol;Acc:20471]

Sequence

>retro_amel_1716
ATGACATCTGCCTTGGAGAACTACATCAACAAAACTGTTGTGGTTATTACTTCTGAGGAGAGAATGATTGTGGGAACACT
GCAAGGTTTTAACCAGACCATTAACTTGAGTTTGGATGAAAGCCATGAACTAGTGTTCAGCTCTTCACAGGAGTAAAACA
AGTGGTGCTAGGGATATACATCACAACAAGTCACAACGTTGCAGTCTTTGGAGAAATTGATGAAGAAACAGATCCTGTAC
TTGATATGGGGAATATTGGAGCAGAACTTCTAAACTCTGTAGCACAC

Alignment

ORF - retro_amel_1716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTSALENYINRTVAVITSDGRMIVGTLKGFDQTINLILDESHERVFSSSQ-GVEQVVLGLYIVRGDNVAV
          MTSALENYIN.TV.VITS..RMIVGTL.GF.QTINL.LDESHE.VFSSSQ.GV.QVVLG.YI....NVAV
Retrocopy MTSALENYINKTVVVITSEERMIVGTLQGFNQTINLSLDESHELVFSSSQ<GVKQVVLGIYITTSHNVAV

Parental  IGEIDEETDSALDLGNIRAEPLNSVAH
          .GEIDEETD..LD.GNI.AE.LNSVAH
Retrocopy FGEIDEETDPVLDMGNIGAELLNSVAH

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_1716 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1716 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001162	1 retrocopy	retro_amel_1716 ,
Echinops telfairi	ENSETEG00000011594	1 retrocopy	retro_etel_491,
Felis catus	ENSFCAG00000023642	1 retrocopy	retro_fcat_1993,
Myotis lucifugus	ENSMLUG00000006837	1 retrocopy	retro_mluc_161,
Macaca mulatta	ENSMMUG00000015822	1 retrocopy	retro_mmul_2010,
Mustela putorius furo	ENSMPUG00000007100	1 retrocopy	retro_mputfur_1440,
Oryctolagus cuniculus	ENSOCUG00000017359	2 retrocopies	retro_ocun_1715, retro_ocun_954,
Otolemur garnettii	ENSOGAG00000013377	1 retrocopy	retro_ogar_1071,
Ochotona princeps	ENSOPRG00000014809	2 retrocopies	retro_opri_1033, retro_opri_227,
Sarcophilus harrisii	ENSSHAG00000018435	1 retrocopy	retro_shar_535,
Ictidomys tridecemlineatus	ENSSTOG00000009039	3 retrocopies	retro_itri_1623, retro_itri_364, retro_itri_679,