RetrogeneDB ID: retro_amel_298

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192378.1:2943794..2944190(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11ORF51
• Ensembl ID: ENSAMEG00000010843
• Aliases: None
• Description: None

Sequence

>retro_amel_298
CTTCAGCTGACCCTTTACCTCAGTCTAGGAGCCACGTCCACCTTGTTTCCCTCACTCTTCCCCGTATGACTGAGACACTG
TGGTTCAATCTGGATTGGCCCCGTGTGGACGAGACGGAGCTGCGGAGCAGAAAGAACATGACCATCGAGCCTGACTCCAG
AGCACCGCACACAGAGATGGCAACCTGGTGTTTACTGGCAAGCTGTCCTGAGAGCACTGTGACGATAAGGAGGAAGAGGA
TGAAGATGATGATGAGGATGGTGAAGAGGACAATGAGGACGATGAGGACATGCAGGACGTGGATGAGAGAATGCCTACAA
GGAGTCACCAGAAGCTGGAGAGGTCAATGAGGTGGACAAGGGAGGCAAGGAACAGGATCAGGCCCAGTGGATAATC

Alignment

ORF - retro_amel_298 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IHLALYLSLGAMSTLFPSLFP-RVTETLWFNLDRPCVEETELQ-QQEQ-QHQAWLQSIAEKDNNLVPIGK
          ..L.LYLSLGA.STLFPSLFP.R.TETLWFNLD.P.V.ETEL...Q....H.A.LQS.A..D.NLV..GK
Retrocopy LQLTLYLSLGATSTLFPSLFP<RMTETLWFNLDWPRVDETELR<EQKEHDHRA*LQSTAHRDGNLVFTGK

Parental  PASEHYDDEEEEDEDDDEDSEEDSEDDEDMQDMDEM-NDYNESPDDGEVNEVDMEGNEQDQDQWMI
          ...EH.DD.EEEDEDDDED.EED.EDDEDMQD.DE..N.Y.ESP..GEVNEVD..G.EQDQ.QW.I
Retrocopy LS*EHCDDKEEEDEDDDEDGEEDNEDDEDMQDVDER<NAYKESPEAGEVNEVDKGGKEQDQAQWII

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_298 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_298 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010843	1 retrocopy	retro_amel_298 ,
Bos taurus	ENSBTAG00000002999	2 retrocopies	retro_btau_252, retro_btau_269,
Canis familiaris	ENSCAFG00000005781	1 retrocopy	retro_cfam_1752,
Equus caballus	ENSECAG00000021041	1 retrocopy	retro_ecab_470,
Felis catus	ENSFCAG00000005321	1 retrocopy	retro_fcat_1350,
Homo sapiens	ENSG00000110200	1 retrocopy	retro_hsap_4780,
Gorilla gorilla	ENSGGOG00000012501	2 retrocopies	retro_ggor_1999, retro_ggor_2977,
Myotis lucifugus	ENSMLUG00000014120	1 retrocopy	retro_mluc_238,
Macaca mulatta	ENSMMUG00000016270	1 retrocopy	retro_mmul_2551,
Mustela putorius furo	ENSMPUG00000010260	1 retrocopy	retro_mputfur_596,
Nomascus leucogenys	ENSNLEG00000017234	1 retrocopy	retro_nleu_1100,
Pongo abelii	ENSPPYG00000003646	2 retrocopies	retro_pabe_2388, retro_pabe_3720,
Pteropus vampyrus	ENSPVAG00000015797	1 retrocopy	retro_pvam_404,
Sorex araneus	ENSSARG00000004171	2 retrocopies	retro_sara_444, retro_sara_686,
Tarsius syrichta	ENSTSYG00000014179	1 retrocopy	retro_tsyr_35,
Tursiops truncatus	ENSTTRG00000010773	1 retrocopy	retro_ttru_277,