RetrogeneDB ID: retro_amel_1066

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192877.1:618367..619015(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000004279
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMB1
• Ensembl ID: ENSAMEG00000017047
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]

Sequence

>retro_amel_1066
CCTTTGCAGCTGTGCTTCTCACGCTATGCTTTCAATGGAGGTACTGGTATTGGTAATCACAGGAGAAGATTTTTCAGTTG
TTGCTTCTGACACTCGATGGAGTGAAGCATTTTTAATTCACACCTGGGAAAGCCCCAAGTGTTACAAATTAACAGACAAA
ACAGTCATTGGATGCAGCGGTTTTCATGGCGACTATCTTACCCTGACCAAGATGACTGATGCAAGACTAAAGATGTATAA
GCATTCTAATAACAAGACCATGATTACAGGGGCAATTGCTGCCATGCTGTTGACAATCCTCTATTCGAGGCACTTCTTTC
CATACTATGTTTACAACATCATCCGGGGACTGGGTGAAGGGAAAGGAGCTGTGTACAACTTTGACCTGGTCGGGTCCTAC
CACAGAGACTCTTTCAAGACTGGAGGCTCAGCAGGGGCCACGCTACAGCCCGTGCTTGACCACCAGGTTGGTTTTAAGAA
CATGCAGAATATGGACCATGTCCCACTGTCCTTGGACAGAGTCGTGCGTCTTGTGAAAGATGTCTTCATTTCTGCGGTGG
AGAGGGACGGTTTCACTGGGGGTGCACTGGGATCTGCATCATGATCGAGGAGAGCATCAGGGAGGATGCTGTTCCCCTGA
GGAAGGAT

Alignment

ORF - retro_amel_1066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.54 %
• Parental protein coverage: 90.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PLQLRFSPYAFNGGT-VLAIAGEDFSIVASDTRLSEGYSVHTRDSPKCYKLTDKTVIGCSGFHGDCLTLT
          PLQL.FS.YAFNGGT.VL.I.GEDFS.VASDTR.SE....HT..SPKCYKLTDKTVIGCSGFHGD.LTLT
Retrocopy PLQLCFSRYAFNGGT>VLVITGEDFSVVASDTRWSEAFLIHTWESPKCYKLTDKTVIGCSGFHGDYLTLT

Parental  KIIEARLKMYKHSNNKTMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEEGKGAVYSFDPVGSYQRDSF
          K...ARLKMYKHSNNKTM.TGAIAAML.TILYSR.FFPYYVYNII.GL..EGKGAVY.FD.VGSY.RDSF
Retrocopy KMTDARLKMYKHSNNKTMITGAIAAMLLTILYSRHFFPYYVYNIIRGLG-EGKGAVYNFDLVGSYHRDSF

Parental  KAGGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYTGDAL-RICIVTKEGIR
          K.GGSA.A.LQP.LD.QVGFKNMQN..HVPLSLDR..RLVKDVFISA.ERD..TG.AL..ICI...E.IR
Retrocopy KTGGSAGATLQPVLDHQVGFKNMQNMDHVPLSLDRVVRLVKDVFISAVERDGFTGGAL<GICIMIEESIR

Parental  EETVPLRKD
          E..VPLRKD
Retrocopy EDAVPLRKD

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_1066 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1066 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 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066 ,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,