RetrogeneDB ID: retro_amel_1329

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193202.1:187360..187869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCD2
• Ensembl ID: ENSAMEG00000017075
• Aliases: None
• Description: programmed cell death 2 [Source:HGNC Symbol;Acc:8762]

Sequence

>retro_amel_1329
ACAGATCATCAGGACAGTTGAGTTCCAGACCGCCACTTTCTTTTTCCAGGATTTGAAACCGTAATGGAAACAGAAGCTGG
GATTACACCTGAAGTTGTAGAAAAGGATGGTGTCACACAGATTACAGGAAGTGTGGGAGAAGCTCCTGAAAAAGAACTGG
ATTCCATACTGAAACATGAATCCGGGGTAGATAACATTTTGCAGAAGTTTAAACCCAAAATAGCTTTTGAATCGAGACAA
ATTCTCAGAGATTGGCAGAGGGATTGTCCTCATCTGGATTCCTGGTGAAAATATCCCTCAACAAAAGGACATTCCAGATT
GCCCCTCTCGTGCCAAGAGACTAGTTGAATTCCAGGCCGTGTCTCAGCAGCTCGGCTACCTCGAGGCAGACATACTGGGA
ACACGTGTTGGTGAGGCCACCGGGCTGGCCTCCCCGGTGCTCAAAGCTATAGACTGGGCATTGGCTACACAGAGCAATTC
GTATGAAGCAAGATGTAACAGACACACCT

Alignment

ORF - retro_amel_1329 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.8 %
• Parental protein coverage: 50.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SDYLERTIPDHNFLFPEFEIVIETEDEITPEVVEKENESEIMGSMGEAPEEELDSMAKHESREDKIFQKF
          .D......PD..FLFP.FE.V.ETE..ITPEVVEK.....I.GS.GEAPE.ELDS..KHES..D.I.QKF
Retrocopy TDHQDS*VPDRHFLFPGFETVMETEAGITPEVVEKDGVTQITGSVGEAPEKELDSILKHESGVDNILQKF

Parental  KTKVALEPEQVLR-YGRGITPIWISGENIPQEEDIPHCPCGAKRIFEFQVMPQLLNHLKADRL-GRSVDW
          K.K.A.E..Q.LR..GRGI..IWI.GENIPQ..DIP.CP..AKR..EFQ...Q.L..L.AD.L.G.....
Retrocopy KPKIAFESRQILR>IGRGIVLIWIPGENIPQQKDIPDCPSRAKRLVEFQAVSQQLGYLEADIL<GNTCW*

Parental  GVLAVFTCAESCRLGIGYTEEFV-WKQDITNTP
          G..A....A.S.RLGIGYTE.FV..KQD.T.TP
Retrocopy GHRAGLPGAQSYRLGIGYTEQFV<MKQDVTDTP

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_1329 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1329 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 15 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017075	2 retrocopies	retro_amel_1329 , retro_amel_1404,
Callithrix jacchus	ENSCJAG00000020634	1 retrocopy	retro_cjac_3946,
Equus caballus	ENSECAG00000016819	1 retrocopy	retro_ecab_533,
Felis catus	ENSFCAG00000007037	2 retrocopies	retro_fcat_305, retro_fcat_749,
Homo sapiens	ENSG00000071994	1 retrocopy	retro_hsap_4305,
Gorilla gorilla	ENSGGOG00000028229	2 retrocopies	retro_ggor_2876, retro_ggor_899,
Microcebus murinus	ENSMICG00000007474	1 retrocopy	retro_mmur_108,
Macaca mulatta	ENSMMUG00000019916	1 retrocopy	retro_mmul_1137,
Mustela putorius furo	ENSMPUG00000007227	2 retrocopies	retro_mputfur_621, retro_mputfur_707,
Nomascus leucogenys	ENSNLEG00000000295	2 retrocopies	retro_nleu_1458, retro_nleu_2633,
Otolemur garnettii	ENSOGAG00000014002	2 retrocopies	retro_ogar_2090, retro_ogar_2288,
Pongo abelii	ENSPPYG00000017193	2 retrocopies	retro_pabe_3505, retro_pabe_958,
Pan troglodytes	ENSPTRG00000018828	2 retrocopies	retro_ptro_2915, retro_ptro_788,
Pteropus vampyrus	ENSPVAG00000010822	1 retrocopy	retro_pvam_1150,
Sus scrofa	ENSSSCG00000025312	2 retrocopies	retro_sscr_303, retro_sscr_450,