RetrogeneDB ID: retro_amel_1129

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192929.1:1146674..1147127(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLP2
• Ensembl ID: ENSAMEG00000012288
• Aliases: None
• Description: proteolipid protein 2 (colonic epithelium-enriched) [Source:HGNC Symbol;Acc:9087]

Sequence

>retro_amel_1129
ATGGTGGAGTCTGAGCGCCTCTCAGCCCGTGGCTGTTGGGCTGTCTTCACCAACTTTTTGTGCACCAGAAAGGGAATTCT
CCTATTTGCTGAGATTATACTGTGCTTGCTGATTCTAATCTGGTTCAGCTTCTCAACGCCAGAATACTCCTCTCTGTCGG
TGGTTGAGATGATCCTTGCTGAGATCTTCTTTGTCATCTACATGTGTGACCTACCCACCAAGATACAATACATCAACTGG
CCTTGGACTGATTTCTTCCGATCCCTCATTGCAGTCACCCTCTACCTAATCACCTCCATTGTTGTCCTTGTCGAGAGAGG
AAATCGCTCTGTAATCATTGCAGGGGCCCTGGGCCTCGTGGCTGTGTGCCTCTTTGGCTATGATGCCTACATCACCTACC
CCTTGAAGTAATAAAGACATACAGCAGCCCCGACTGATTGTGCAGATGATCCA

Alignment

ORF - retro_amel_1129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.47 %
• Parental protein coverage: 99.34 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADSERLSAPGCWAACTNFSRTRKGILLFAEIILCLVILICFSASTPGYSSLSVVEMILAAIFFVIYMCD
          M..SERLSA.GCWA..TNF..TRKGILLFAEIILCL.ILI.FS.STP.YSSLSVVEMILA.IFFVIYMCD
Retrocopy MVESERLSARGCWAVFTNFLCTRKGILLFAEIILCLLILIWFSFSTPEYSSLSVVEMILAEIFFVIYMCD

Parental  LHTKIQIINWPWSDFFRTLIASILYLITSIVVLVEGGNHSKIIAGVLGLIATSLFGYDAYITFPLRQQRH
          L.TKIQ.INWPW.DFFR.LIA..LYLITSIVVLVE.GN.S.IIAG.LGL.A..LFGYDAYIT.PL...RH
Retrocopy LPTKIQYINWPWTDFFRSLIAVTLYLITSIVVLVERGNRSVIIAGALGLVAVCLFGYDAYITYPLK**RH

Parental  TAAPTDPADGP
          TAAPTD.AD.P
Retrocopy TAAPTDCADDP

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_1129 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1129 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 13 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012288	1 retrocopy	retro_amel_1129 ,
Bos taurus	ENSBTAG00000016093	3 retrocopies	retro_btau_1574, retro_btau_73, retro_btau_810,
Canis familiaris	ENSCAFG00000015798	1 retrocopy	retro_cfam_933,
Felis catus	ENSFCAG00000003820	2 retrocopies	retro_fcat_1547, retro_fcat_256,
Homo sapiens	ENSG00000102007	1 retrocopy	retro_hsap_3411,
Loxodonta africana	ENSLAFG00000004483	1 retrocopy	retro_lafr_427,
Macaca mulatta	ENSMMUG00000023022	1 retrocopy	retro_mmul_2124,
Mustela putorius furo	ENSMPUG00000013817	3 retrocopies	retro_mputfur_107, retro_mputfur_462, retro_mputfur_969,
Mus musculus	ENSMUSG00000031146	1 retrocopy	retro_mmus_94,
Nomascus leucogenys	ENSNLEG00000001317	1 retrocopy	retro_nleu_2887,
Otolemur garnettii	ENSOGAG00000003865	3 retrocopies	retro_ogar_2568, retro_ogar_2865, retro_ogar_473,
Pan troglodytes	ENSPTRG00000021885	1 retrocopy	retro_ptro_2316,
Tursiops truncatus	ENSTTRG00000016968	2 retrocopies	retro_ttru_1586, retro_ttru_767,