RetrogeneDB ID: retro_amel_43

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193156.1:859150..860194(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000019207
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000006392
• Aliases: None
• Description: None

Sequence

>retro_amel_43
ATGCACCCCAAGGCCTTCCTTCTTTCCATGCTTGTAGTCACTATGCTGTGGGGAGCGGCCCCCATCCGGGGGCTCATTCG
AGCGACTTCTGACCACAATAACAGCATGGACTTTGCAGACCTTCCAGCTCTCTTTGGGTCTGCCTTGAGCCATGAGGGAC
TTCAGGGGTTCCTTGTGGAGGCTCAGCCAGCCAACGCCTGCAGCCCCGTTGCCCCGCCACCCCAAGCCACGGTCAACGGG
TCAGTCTTTATTGCACTTCTTCGGAGATTCGACTGCAACTTTGACCTCAAGGTCCTAAACGTTCAGAAGGCTGGGTATGG
TGCAGCTGTGGTACACAATGTAAATTCCAATGAACTTCTGAATATGGTGTGGAACAGTGAGGAAATCCAGCAGCAGATCT
GGATCCCGTCTGTGTTTATTGGGGAAAGGAGTTCCAAGTACCTGCGTGCCCTCTTTGTCTATGAGAAGGGAGCTCAAGTG
CTTCTGGTCCCAGACAATAACTTCCTCCTGGGCTATTGCCTCATCCTTTTCACAGGGGTTGTGGGACTGCTGATTTTGGC
CATGGGAGCAGGGCTGATAGCTCGTTTTATCCAGCACCAGAAGCAGCTCCAGATGAATCGACTGACCAAAGAGCAACTGA
AGCGGATTCCTATACACGACTATCAGAAGGGAGACCAGTACGATGTCTGTGCCATTTGCCTGGCCGAATACGAGGATGGA
GATAAGCTGAGGGTACTTCCCTGCGCTCATGCTTATCACAGCCGCTGTGTGGACCCCTGGCTCACTCAGACCCGGAAGAC
CTGCCCCATCTGCAAGCAGCCTGTTCAGAGGGGTCCTGGAGAAGGGGAGCAAGAGGGAGAAACGCAGGGGCAAGTGGGTG
ATGAGGAAGGGGAGCCAAGGGACCACCCCGCCACAGAACGGACCCCTCTTCTGGGCTCCAGCCTCACACGTCCCACATCC
TTTGGCTCCCTAGCCCCAGCCCCCCTTGTTTTTCCTGGATCTTCAATAGATCCATCACCCTCCCCATCCTCTTCTTCCTC
TTCT

Alignment

ORF - retro_amel_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82. %
• Parental protein coverage: 99.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHPAAFPLPVVVAAVLWGASPARGLIRATSDHNASMDFADLPALFGAALSQEGLQGFLVEAHPANACSPI
          MHP.AF.L...V...LWGA.P.RGLIRATSDHN.SMDFADLPALFG.ALS.EGLQGFLVEA.PANACSP.
Retrocopy MHPKAFLLSMLVVTMLWGAAPIRGLIRATSDHNNSMDFADLPALFGSALSHEGLQGFLVEAQPANACSPV

Parental  APPPPAPVNGSVFIALLRRFDCNFDLKVLNAQKAGYGAAVVHNVNSDELLNMVWNSEEIQQQIWIPSVFI
          APPP.A.VNGSVFIALLRRFDCNFDLKVLN.QKAGYGAAVVHNVNS.ELLNMVWNSEEIQQQIWIPSVFI
Retrocopy APPPQATVNGSVFIALLRRFDCNFDLKVLNVQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFI

Parental  GERSSEYLRALFVYEKGARVLLVPDSSFPLGYYVIPFTGIVGLLVLAMAAVMVVRCIQHRKRLQRNRLTK
          GERSS.YLRALFVYEKGA.VLLVPD..F.LGY..I.FTG.VGLL.LAM.A....R.IQH.K.LQ.NRLTK
Retrocopy GERSSKYLRALFVYEKGAQVLLVPDNNFLLGYCLILFTGVVGLLILAMGAGLIARFIQHQKQLQMNRLTK

Parental  DQLKQIPTHDYQKAPGDQYDVCAICLDEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPVHRG
          .QLK.IP.HDYQK..GDQYDVCAICL.EYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPV.RG
Retrocopy EQLKRIPIHDYQK--GDQYDVCAICLAEYEDGDKLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPVQRG

Parental  PGD-EDEDETQGQEGDEEGEPRDQPASERTPLLSSSPTLATSFGSLAPTPLIFPGSSTDPPPSPTSSSAA
          PG..E.E.ETQGQ.GDEEGEPRD.PA.ERTPLL.SS.T..TSFGSLAP.PL.FPGSS.DP.PSP.SSS..
Retrocopy PGEGEQEGETQGQVGDEEGEPRDHPATERTPLLGSSLTRPTSFGSLAPAPLVFPGSSIDPSPSPSSSSSS

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_43 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_43 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43 ,
Ailuropoda melanoleuca	ENSAMEG00000010433	1 retrocopy	retro_amel_311,
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84,
Dipodomys ordii	ENSDORG00000011757	2 retrocopies	retro_dord_277, retro_dord_432,
Equus caballus	ENSECAG00000021567	1 retrocopy	retro_ecab_583,
Felis catus	ENSFCAG00000011173	1 retrocopy	retro_fcat_99,
Mustela putorius furo	ENSMPUG00000010940	1 retrocopy	retro_mputfur_95,
Pteropus vampyrus	ENSPVAG00000003781	1 retrocopy	retro_pvam_1206,
Sorex araneus	ENSSARG00000011216	1 retrocopy	retro_sara_517,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,