RetrogeneDB ID: retro_amel_743

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192603.1:390234..390665(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000006128
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSAMEG00000000715
• Aliases: None
• Description: Proteasome subunit beta type [Source:UniProtKB/TrEMBL;Acc:G1L1I8]

Sequence

>retro_amel_743
GAAGCCGGTGAGTCCCACGCTCAGTCTTCTTGGCCTCCCGCCACTATGGAGCACCTCATCCCGGGCCCCGACTAAGTCCT
TCTCGCCTCCAACCAGGTGGTCGCTAGCAGTGCTGTCCAGATGAAGGACGATATGACAAGATGTTTAAGAGGAATGGAGA
AATCTTTCTCCTCTGTGTTGGAGAGGCTGGAGACACAGTACAGTTTGCAGAATATATTCAGCAAAATGAGCCCCTTTATA
AAGGGCAAAATCATTACGAACGGTCTCCCATAGCAGCAGCTAATTTCCCACACCAACACGTGACTGACTATCTTCGGAGT
CGGACCCCATGTCATGTTAACCTCCTCCTGGCCGGCTCCGATGAGCACGAGGGCCCAGCTATCTACTACACGGACTACCT
GGCAGCATTGGCCAAGGCCCCTTTTGCAGCC

Alignment

ORF - retro_amel_743 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 64.04 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EKPASPTLSSRPPATMEYLIGIQGPDYVLVASDQVAASSIVQMKDD-HDKMFKMSEKILLLCVGEAGDTV
          E...S...SS.PPATME.LI...GPD.VL.AS.QV.ASS.VQMKDD..DKMFK....I.LLCVGEAGDTV
Retrocopy EAGESHAQSSWPPATMEHLI--PGPD*VLLASNQVVASSAVQMKDD<YDKMFKRNGEIFLLCVGEAGDTV

Parental  QFAEYIQKNVQLYKMRNGYELSPTAAANFTRRNLADCLRSWTPYHVNLLLAGFDEHEGPALYYMDYLAAL
          QFAEYIQ.N..LYK..N.YE.SP.AAANF......D.LRS.TP.HVNLLLAG.DEHEGPA.YY.DYLAAL
Retrocopy QFAEYIQQNEPLYKGQNHYERSPIAAANFPHQHVTDYLRSRTPCHVNLLLAGSDEHEGPAIYYTDYLAAL

Parental  AKAPFAA
          AKAPFAA
Retrocopy AKAPFAA

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_743 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_743 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743 ,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76, retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403, retro_tsyr_912,