RetrogeneDB ID: retro_amel_241

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192364.1:3830762..3831231(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSAMEG00000005395
• Aliases: None
• Description: None

Sequence

>retro_amel_241
GCCTGTCTGTGCACTATGGACTTCGCAGAGTGGTCAAGCTATGTCAAGGGCATCGTGAAGAACATCACCCATGACCCAAC
CTGGGGTGTGCCGCTCACTGAGGTGGACTTCTGGGACCCTTACTGGCTTAAGAAGTGGAGGGAGCTGTTCATCGCTGCCA
AGGGCATCCACACTGGCCAGTCGTGTACTGTGCAAGGAGAACCAGCTCAACATAGGCAATGTGCTCCCGGTGGGCAGTAT
GCCTGAGGGCGTCATTGTGTGTTGCTGGGGGAGAAGCCTGGTGACTGGTGCAAGTTGGCCTGAGCCTCTGGAAACTACAC
CGCTATCATTTCCCACAACCCTGAGACCAGGAAGACCCAAGTGAAGCTGCCCTTTTGGTTCAAAGAAGGTCTTTTCTTCA
GCCAACAGAGCTATGGTAGGTGTGGTGGCTGGAGGTGGCCACACTGACAAGCCCATTCTGCAGTCTGGC

Alignment

ORF - retro_amel_241 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.19 %
• Parental protein coverage: 61.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKVVFRDPYRFKKRTELFIAAEGIHTGQ-FVYCG-KKA
          A.L...DFAE...Y.KGIVK.I.HDP..G.PL..V.F.DPY..KK..ELFIAA.GIHTGQ..VYC..K..
Retrocopy ACLCTMDFAEWSSYVKGIVKNITHDPTWGVPLTEVDFWDPYWLKKWRELFIAAKGIHTGQ<VVYCA<KEN

Parental  QLNIGNVLPVGTMPEGTIVCC-LEEKPGDRGKLARASGNYATVISHNPETKKTRVKL-PSGSKKVISSAN
          QLNIGNVLPVG.MPEG.IVCC.L.EKPGD..KLA.ASGNY...ISHNPET.KT.VKL.P.GSKKV.SSAN
Retrocopy QLNIGNVLPVGSMPEGVIVCC<LGEKPGDWCKLA*ASGNYTAIISHNPETRKTQVKL>PFGSKKVFSSAN

Parental  RAVVGVVAGGGRIDKPILKAG
          RA.VGVVAGGG..DKPIL..G
Retrocopy RAMVGVVAGGGHTDKPILQSG

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_241 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_241 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Ailuropoda melanoleuca	ENSAMEG00000005395	1 retrocopy	retro_amel_241 ,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Echinops telfairi	ENSETEG00000007104	4 retrocopies	retro_etel_1100, retro_etel_264, retro_etel_296, retro_etel_916,
Homo sapiens	ENSG00000161016	1 retrocopy	retro_hsap_2851,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Tursiops truncatus	ENSTTRG00000013858	1 retrocopy	retro_ttru_1147,