RetrogeneDB ID: retro_amel_1136

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192948.1:289..772(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM64A
• Ensembl ID: ENSAMEG00000006997
• Aliases: None
• Description: family with sequence similarity 64, member A [Source:HGNC Symbol;Acc:25483]

Sequence

>retro_amel_1136
CAGTCCTGCCAAAGTGGCACCAAGTGGCTGTTGGCAACCCAGGTGAGAGCCAGGAGCATGTCCTAGAGAATCTAGCAGTC
CTGCCGAAGTGGCACCAAGTGGTTGTTGGCAACCCAGGTGAGAGCCAGGAGGAGGAGGAGAGGGGTACAGAAGGGCAATA
GCCCCGTTCACAACCTGAGCCAGAAGAGCACCCACCTGTCTGAAGCTTCCCCCGCCCCCTCAATCCTGGACCTGTGGATG
AGGGAATATCGCCGACCCGCTATCCAGACAGGCCCATAAGCGTACCCACTGCAACCTTCCTCCAGGAGGGAGACTGCTTT
CTGGATTCCCTATTCCTTGACAGAACCCCTCTGCTCCCCAAGTGAGTCTGACCTAGAGCCTTTGGGAGCTGGAATTCAGC
ATCTCCAGAAGCTGTCACAAGAACTGGTTGGGGCCATCGTAACTGAAGAGACCAGGGACATGACTGTTTCTTTCATTTGT
GAC

Alignment

ORF - retro_amel_1136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.95 %
• Parental protein coverage: 70.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESPESGQQGLQAAARSAKNALGAVSQRIQESCHSGTKWLAETQVKARRRRRGAQKGGSPPPRSLSQESAR
          .S..SG...L.A....A.......S.RI..SC.SGTKWL..TQV.ARRRRRG.QKG.S.P...LSQ.S..
Retrocopy QSCQSGTKWLLATQVRARS----MS*RI*QSCRSGTKWLLATQVRARRRRRGVQKGNS-PVHNLSQKSTH

Parental  LSAAAPAYAALDPGERDGRRLSAHAGPRAHPLR-RSRREAALRSPYSATEPLCSPSESDGDPEPVGARLQ
          LS.A.PA...LD...R..RR.....GP.A.PL...SRRE.A...PYS.TEPLCSPSES..D.EP.GA..Q
Retrocopy LSEASPAPSILDLWMREYRRPAIQTGP*AYPLQPSSRRETAFWIPYSLTEPLCSPSES--DLEPLGAGIQ

Parental  HLQRPSQELDDAIVVEESNDMTVSLIRD
          HLQ..SQEL..AIV.EE..DMTVS.I.D
Retrocopy HLQKLSQELVGAIVTEETRDMTVSFICD

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_1136 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1136 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006997	1 retrocopy	retro_amel_1136 ,
Homo sapiens	ENSG00000129195	3 retrocopies	retro_hsap_2371, retro_hsap_3030, retro_hsap_3071,
Gorilla gorilla	ENSGGOG00000012309	3 retrocopies	retro_ggor_1801, retro_ggor_2091, retro_ggor_2109,
Macaca mulatta	ENSMMUG00000017760	3 retrocopies	retro_mmul_1778, retro_mmul_1935, retro_mmul_959,
Mus musculus	ENSMUSG00000020808	1 retrocopy	retro_mmus_3385,
Nomascus leucogenys	ENSNLEG00000009164	3 retrocopies	retro_nleu_361, retro_nleu_725, retro_nleu_843,
Otolemur garnettii	ENSOGAG00000027433	1 retrocopy	retro_ogar_1490,
Pongo abelii	ENSPPYG00000007877	3 retrocopies	retro_pabe_2141, retro_pabe_2509, retro_pabe_2545,
Pan troglodytes	ENSPTRG00000008641	3 retrocopies	retro_ptro_1734, retro_ptro_2044, retro_ptro_2070,
Rattus norvegicus	ENSRNOG00000008040	1 retrocopy	retro_rnor_1325,