RetrogeneDB ID: retro_amel_1348

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193233.1:42425..43062(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000003257
• Aliases: None
• Description: None

Sequence

>retro_amel_1348
TCCTTTCCACCCAGTGGTAATGAGCATCCTAAAGATCTCAACCGAGGCCTGAAGAAATTCACGCTTGCTGCCTCTTGCAT
GTTGTTATGAAAGGAACTCTCTAGGAACCATGCTGCGATTTCAGCAAGCAGATGGCAGTAGTTCTTAACAAACATAATTT
TTGGTCTAGCAGTTTTGATATCCTCTCAGATGAAGAAGTTCATCGGGACCTCAAAACTTATTCCAGTTGGCCCACCTGCC
CCCAGCTCTGTTTCTGGAGAGCTCATAGGAGGATTTGTTTGAATTAAGAAGCTAGAGACATCTGAAGAACTAGATACAAT
TTGCCCCAAAGCTCCCAAATTAGAGGAAAGGCTCAAAGTACTGACAAATAAAGCTTCTGAAATGCTCTTTATGAAAAGCA
AGAGGAAGCAAAATGTGGATGCAGCTAACAAATTCTGGAACTACTAAATACTACTGGTGTTGGATAGGAGATATTTGATA
GATCGGAGGACGAGGAATTTCGACAACAGTTAAAAGCTCCCTCAAACTGGCCCACACACCCTCAGCGGCACGTGAAAGGC
GAGCTTGATGAACATCTGCATATCTGAAGAAGCTGAGAGGAAATGGTGCTTTGCTGCCCAAACTAAAAGGAGAAAAT

Alignment

ORF - retro_amel_1348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 68.79 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SFPPSGNEHPKEDLSLRLKKLTHAAPCMLF-MKGSPQEPRCGFSKQMVEILNKHNIQFSSFDIFSDEEVR
          SFPPSGNEHPK.DL...LKK.T.AA.CML..MKG...EP.C.FSKQM...LNKHN...SSFDI.SDEEV.
Retrocopy SFPPSGNEHPK-DLNRGLKKFTLAASCMLL<MKGTL*EPCCDFSKQMAVVLNKHNFWSSSFDILSDEEVH

Parental  QGLKTYSNW-PTYPQLYVSGELIGGLDIIKELEASDELDTIC-PKAPKLEERLKVLTNKASVMLFMKGNK
          ..LKTYS.W.P..P...VSGELIGG...IK.LE.S.ELDTIC.P............T.K.S.........
Retrocopy RDLKTYSSW>PPAPSS-VSGELIGGFV*IKKLETSEELDTIC<PQSSQIRGKAQS-TDK*SF*NALYEKQ

Parental  QEAKCGFSKQILEILNSTGVEYETFDILEDEEVRQGLKTYSNWPTYPQLYVKGELVGGLDI-VKELRDNG
          .EAKCG.S.QILE.LN.TGV..E.FD..EDEE.RQ.LK..SNWPT.PQ..VKGEL...L.I..K.LR.NG
Retrocopy EEAKCGCS*QILELLNTTGVG*EIFDRSEDEEFRQQLKAPSNWPTHPQRHVKGELDEHLHI<LKKLRGNG

Parental  ELLPVLKGEN
          .LLP.LKGEN
Retrocopy ALLPKLKGEN

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_1348 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1348 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348 ,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,