RetrogeneDB ID: retro_amel_1193

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193023.1:428702..429090(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM147
• Ensembl ID: ENSAMEG00000000375
• Aliases: None
• Description: transmembrane protein 147 [Source:HGNC Symbol;Acc:30414]

Sequence

>retro_amel_1193
ATGACCCTGCTCCATGGTGGGAGCTGCTTCACCCGGGCCTACTTCCCTGCTTCATCACCTACAAGCACAGCAGCCTGAAT
GAGTACAACACCTTCTGGAAACGCGCGCAGGCCAGGGTCACCCACCTCTTCATGCAGCCGTGCAAGATGCTGTTCTTGGC
CATTTTTTTTGTCCCCACCCAGGAAGGTGGCACCTATGACTTCATTGGGGAGGTCATGAAGCCAGAGTGGATATAACAGA
CCCGATAGACCTAAGCCTTGTCATGTCTTTGAATGCAGGCATGGGGGAGTACAAGATCACGGCTGCTGCCCTGGGCTGGA
CCACCCCCGAGCTCACTGTGTTCTGCTGAAATGCCCTCTGGGTTGGAGCCCTGGGCTTTGAGTTTGAC

Alignment

ORF - retro_amel_1193 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.15 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTLFHFGNCFALAYFPY-FITYKCSGLSEYNAFWKCVQAGVTYLFVQLCKMLFLATFF-PTWEGGIYDFI
          MTL.H.G.CF..AYFP..FITYK.S.L.EYN.FWK..QA.VT.LF.Q.CKMLFLA....PT.EGG.YDFI
Retrocopy MTLLHGGSCFTRAYFPA<FITYKHSSLNEYNTFWKRAQARVTHLFMQPCKMLFLAXXXVPTQEGGTYDFI

Parental  GEFMK-ASVDVADLIGLNLVMSRNAGKGEYKIMVAALGWATAELIMSRCIPLWVGARGIEFD
          GE.MK.A.VD..D.I.L.LVMS.NAG.GEYKI..AALGW.T.EL.......LWVGA.G.EFD
Retrocopy GEVMK<ARVDITDPIDLSLVMSLNAGMGEYKITAAALGWTTPELTVFC*NALWVGALGFEFD

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_1193 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1193 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 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010132	1 retrocopy	retro_acar_105,
Ailuropoda melanoleuca	ENSAMEG00000000375	1 retrocopy	retro_amel_1193 ,
Bos taurus	ENSBTAG00000015920	1 retrocopy	retro_btau_1546,
Canis familiaris	ENSCAFG00000006960	2 retrocopies	retro_cfam_1070, retro_cfam_1265,
Dasypus novemcinctus	ENSDNOG00000004059	1 retrocopy	retro_dnov_1123,
Felis catus	ENSFCAG00000006373	2 retrocopies	retro_fcat_1489, retro_fcat_224,
Myotis lucifugus	ENSMLUG00000016383	1 retrocopy	retro_mluc_1889,
Mustela putorius furo	ENSMPUG00000006709	1 retrocopy	retro_mputfur_588,
Tarsius syrichta	ENSTSYG00000008207	1 retrocopy	retro_tsyr_56,
Tursiops truncatus	ENSTTRG00000015114	2 retrocopies	retro_ttru_1406, retro_ttru_219,