RetrogeneDB ID: retro_amel_1834

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194683.1:35598..36042(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB6
• Ensembl ID: ENSAMEG00000016075
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 6 [Source:HGNC Symbol;Acc:9543]

Sequence

>retro_amel_1834
TCAGCAGCTGATGCTGTCACTTATCAACTTATTTCCACAGTATTGAGCTGAATGAGCCTCTGCTGGAACAAAATGTAGCC
AGCCTCTTTAAGGAGATGTGTTCTTGATACTGAGAAGACCTGATGGTAGGAATCATCACTGTGGGCTGGGACCCCAAAGA
AGGAAGGCAGGTGTACTCAGTGTTCATGTGGGGTATGATGGTAAGGCAGTACTTTGCCACCAGGGCTCTGGGAGCTCCTA
TCTCTGTGGCCATGTCAACACTACCTACTGGGAAGATATGACCAAGGAAGAGTGTCAGCAATTCATATCAATGCTCTCAC
TTTGGCCATGGGGTGGGTCAGCTCCAGTGGTAGGGTGATCTGACCAGCAGCCATTATAGAATCAGGACAGGTACTTTTGG
GAGACCAGATTGCCAAACTCACCATTGCCACTTTACCACTTCCC

Alignment

ORF - retro_amel_1834 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.39 %
• Parental protein coverage: 63.6 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AVADAVTYQL-GFHSIELNEPPLVHTAASLFKEMCYRYREDLMAGIIIAGWDPQEGGQVYSVPMGGMMVR
          ..ADAVTYQL..FHSIELNEP.L....ASLFKEMC..Y.EDLM.GII..GWDP.EG.QVYSV.M.GMMVR
Retrocopy SAADAVTYQL<YFHSIELNEPLLEQNVASLFKEMCS*Y*EDLMVGIITVGWDPKEGRQVYSVFMWGMMVR

Parental  QSFAI-GGSGSSYIYGYVDATYREGMTKEECLQFTA-NALALAMERDGSSGGVIRLAAIAESGVERQVLL
          Q.FA...GSGSSY..G.V..TY.E.MTKEEC.QF...NAL.LAM....SSG.VI..AAI.ESG...QVLL
Retrocopy QYFAT<QGSGSSYLCGHVNTTYWEDMTKEECQQFIS<NALTLAMGWVSSSGRVI*PAAIIESG---QVLL

Parental  GDQIPKFTIATLPPP
          GDQI.K.TIATLP.P
Retrocopy GDQIAKLTIATLPLP

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_1834 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1834 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016075	1 retrocopy	retro_amel_1834 ,
Canis familiaris	ENSCAFG00000015855	1 retrocopy	retro_cfam_2173,
Callithrix jacchus	ENSCJAG00000012010	1 retrocopy	retro_cjac_775,
Loxodonta africana	ENSLAFG00000012859	1 retrocopy	retro_lafr_874,
Macropus eugenii	ENSMEUG00000010676	1 retrocopy	retro_meug_621,
Microcebus murinus	ENSMICG00000014854	2 retrocopies	retro_mmur_140, retro_mmur_718,
Monodelphis domestica	ENSMODG00000005554	1 retrocopy	retro_mdom_799,
Mus musculus	ENSMUSG00000018286	2 retrocopies	retro_mmus_348, retro_mmus_3569,
Rattus norvegicus	ENSRNOG00000019551	1 retrocopy	retro_rnor_56,
Sorex araneus	ENSSARG00000006615	1 retrocopy	retro_sara_689,
Tursiops truncatus	ENSTTRG00000000566	1 retrocopy	retro_ttru_405,