RetrogeneDB ID: retro_amel_1556

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193610.1:360285..360752(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000004066
• Aliases: None
• Description: None

Sequence

>retro_amel_1556
ATGGCAAGTCTCCAGAGGCTGAGTGTCCTGTGAAGTGTGCAAGAAGGCTGAGCTCTGTTTCTTCAAATCCCAGTGGTCAG
ACGTGCTCATGTCTCAGCATTTCTCCAGGACCAAACTACCCCAGAGTGGTGTAGAACACAGCACATTCACCTGTTACTCA
ACCACCATTCTGGTTCCAAGACTACATCTCACCACTGGACTAGTTCGAGGGTTGTCAATGTTTTTCCCCTGAGCCTAATT
CCAGCTGCTTATTTCAATTGTGGCTCTGTAATGGACCACTACTCCCTGGCTGCAGCCCTTGCTCTCCATAGTCAACTGGG
GCCTCGGACAAGTGGTTCCTATGTTCGAGGGGATGCTTTGTAGAAACCTGCCGAGGCAGGTGTTTGGCACTCTCAGCTTT
AACCTTTGCTGCACTTTGTTATCTCAACTATCCTGATGTGAGCATCTGCAAAGCGGTTGCCATGCTG

Alignment

ORF - retro_amel_1556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.25 %
• Parental protein coverage: 98.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASLWRLSALCGAQGGRALFLRIPVVRPAQVSAFLQDQPDPGWCRTQHIHLSPNHYSGSKAASLHWTGER
          MASL.RLS.L...Q.G.ALFL.IPVVR.A.VSAFLQDQ..P.WCRTQHIHL..NH.SGSK..S.HWT..R
Retrocopy MASLQRLSVL*SVQEG*ALFLQIPVVRRAHVSAFLQDQTTPEWCRTQHIHLLLNHHSGSKTTSHHWTSSR

Parental  VVSVLLLGLIPAAYLNPGSAMD-YSLAAALTLHSHWGLGQVVTDYVRGDALQKAAKAGV-LALSALTFAG
          VV.V..L.LIPAAY.N.GS.MD.YSLAAAL.LHS..G.......YVRGDAL.K.A.AGV.LALSALTFA.
Retrocopy VVNVFPLSLIPAAYFNCGSVMDHYSLAAALALHSQLG-PRTSGSYVRGDAL*KPAEAGV<LALSALTFAA

Parental  LCYFNYHDVGICKAVAML
          LCY.NY.DV.ICKAVAML
Retrocopy LCYLNYPDVSICKAVAML

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_1556 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1556 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 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004066	3 retrocopies	retro_amel_1556 , retro_amel_1588, retro_amel_998,
Erinaceus europaeus	ENSEEUG00000013091	1 retrocopy	retro_eeur_336,
Echinops telfairi	ENSETEG00000008424	1 retrocopy	retro_etel_252,
Felis catus	ENSFCAG00000022580	3 retrocopies	retro_fcat_1371, retro_fcat_175, retro_fcat_492,
Homo sapiens	ENSG00000204370	8 retrocopies	retro_hsap_124, retro_hsap_1912, retro_hsap_2132, retro_hsap_2182, retro_hsap_2729, retro_hsap_2784, retro_hsap_355, retro_hsap_3791,
Gorilla gorilla	ENSGGOG00000026496	1 retrocopy	retro_ggor_50,
Loxodonta africana	ENSLAFG00000002763	1 retrocopy	retro_lafr_432,
Myotis lucifugus	ENSMLUG00000012228	3 retrocopies	retro_mluc_2418, retro_mluc_457, retro_mluc_756,
Macaca mulatta	ENSMMUG00000015247	1 retrocopy	retro_mmul_224,
Rattus norvegicus	ENSRNOG00000022980	3 retrocopies	retro_rnor_1529, retro_rnor_1686, retro_rnor_744,
Sus scrofa	ENSSSCG00000015034	3 retrocopies	retro_sscr_1060, retro_sscr_626, retro_sscr_627,
Tursiops truncatus	ENSTTRG00000010520	5 retrocopies	retro_ttru_1554, retro_ttru_238, retro_ttru_616, retro_ttru_633, retro_ttru_885,