RetrogeneDB ID: retro_amel_1613

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193735.1:331926..332396(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BCL7C
• Ensembl ID: ENSAMEG00000007604
• Aliases: None
• Description: None

Sequence

>retro_amel_1613
ATGTTCAAGTGGGTGCCAGTGGCAGACTCCCAGGAGGAGGAGTGACAAAGGGGAAGTGGCAGGACAGAGAGATCCCGAGG
CCTGGAGGGGCGGGGCAGGGTTCCAGTCCCTAAGGGGGTGGCCTTCTCATCCTGCTGGATCTCAATGACGAGAACAGAAA
CTAGAGTTTCCATTTGGAAAGCTCCCTGCAGAAGTGCAACCAGCCCAGCCCTGGGGGCACCCCCCTAGCCAGCCACCCCG
TGTTACCTATGGAACCATTGGAAGACATCTCACAGGGTTCTCAGCCCCCGAGGCTGGGCCAAGAGAGAGATTCTGGGTTA
ACCAGTGCAGGTAGCAGTGATGAACTCCCAGTGCTGACCAAGGAGGAGCCTGTTCTAGAACACCTGGAGGCTGAGGCCCC
TGAAGCTTACCCCATCTTTGAGCCAGTGCCACCTGTCCTGGAAACAGCCCAGGTTGACACAGAGGACTCA

Alignment

ORF - retro_amel_1613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.25 %
• Parental protein coverage: 73.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFKWVPVVDPQEEERRRAGGGAERSRGRERRGR-GASPRGGGPLILLDLNDENSNQSFHSEGSLQKGTEP
          .FKWVPV.D.QEEE..R..G..ERSRG.E.RGR.G.SP.GGG.LILLDLNDEN.N.SFH.E.SLQK...P
Retrocopy MFKWVPVADSQEEE*QRGSGRTERSRGLEGRGR<GSSP*GGGLLILLDLNDENRN*SFHLESSLQKCNQP

Parental  SPGGTPQPSRPVSPAGPPEGVPEDAQPPRLGQERDSGGINAGSTDEPPMLTKEEPVPELLEAEAPEAYPV
          SPGGTP..S.PV.P..P.E......QPPRLGQERDSG...AGS.DE.P.LTKEEPV.E.LEAEAPEAYP.
Retrocopy SPGGTPLASHPVLPMEPLEDISQGSQPPRLGQERDSGLTSAGSSDELPVLTKEEPVLEHLEAEAPEAYPI

Parental  FEPVPPVPEAAQGDTEDS
          FEPVPPV.E.AQ.DTEDS
Retrocopy FEPVPPVLETAQVDTEDS

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_1613 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1613 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 8 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007604	2 retrocopies	retro_amel_1090, retro_amel_1613 ,
Bos taurus	ENSBTAG00000008412	1 retrocopy	retro_btau_618,
Canis familiaris	ENSCAFG00000016715	1 retrocopy	retro_cfam_898,
Dipodomys ordii	ENSDORG00000001676	1 retrocopy	retro_dord_517,
Equus caballus	ENSECAG00000000482	1 retrocopy	retro_ecab_704,
Felis catus	ENSFCAG00000029090	1 retrocopy	retro_fcat_1969,
Macaca mulatta	ENSMMUG00000003225	13 retrocopies	retro_mmul_1247, retro_mmul_1613, retro_mmul_1818, retro_mmul_2108, retro_mmul_2153, retro_mmul_2644, retro_mmul_390, retro_mmul_724, retro_mmul_740, retro_mmul_750, retro_mmul_755, retro_mmul_791, retro_mmul_975,
Mustela putorius furo	ENSMPUG00000011988	1 retrocopy	retro_mputfur_954,