RetrogeneDB ID: retro_amel_164

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192342.1:4606931..4607547(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000005359
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNF8
• Ensembl ID: ENSAMEG00000005062
• Aliases: None
• Description: SNF8, ESCRT-II complex subunit [Source:HGNC Symbol;Acc:17028]

Sequence

>retro_amel_164
TTGCATTGCCGCAGGATGGGAGCCGGCGCCATTGCCAAGAAGAGGCTTGCAGAGGCCAAGTATAAGGAACGAGGAACTGT
CACGGCCGAGGCCCAGCGGGCCCAGATGTCGAAGCAGTTGGACATGTTCAAGACCATCCTGGAGGAATTGGCCGGCAAAC
ACAAGCGGGAGATCCGGAAGGATCCTGAGTTCCGGGTGCAGTTCCAGGACACGTGTGCCCCCTTGGGGTGGATCGTCTGC
CCTCTGGAAAGGATTTTGGTCTGAGACGGTAAGTGTGGGAGCTTTCTATTGCGAGCTGGGAATCCGGATGATTGAAGTGT
GTGTGGCTCCGAAGCTCAGGAATGGAGGTCCGCTAACCCTGGAGGAACTACGCAACACGCGTTAAAGGGAAGGGGCAGAT
TCGCCCAGGATGCCGGCCAAGACGACTCCATCAGGGCCATGGAGAAACTAAAGGCCCTTGGCACTGGCTTCGCGTCATCT
CCGTGGGGGGCGCCCAGCGCATCCAGCGGGCTCCAGCCGAGCTCAAGGCGGATCCTCCTGTGGTGCAGCAGCTGGCGGGA
AGAACGGCTATGTGACTGTCAGTGATAGCAAAGCCCGTCTTAAATGGGAGGCCAAG

Alignment

ORF - retro_amel_164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.34 %
• Parental protein coverage: 80.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MHRRGVGAGAIAKKKLAEAKYKERGTVLAEDQLAQMSKQLDMFKSNLEEFASKHKQEIRKNPEFRVQFQD
          .H.R..GAGAIAKK.LAEAKYKERGTV.AE.Q.AQMSKQLDMFK..LEE.A.KHK.EIRK.PEFRVQFQD
Retrocopy LHCRRMGAGAIAKKRLAEAKYKERGTVTAEAQRAQMSKQLDMFKTILEELAGKHKREIRKDPEFRVQFQD

Parental  MCA-TIGVDPLASG-KGFWSEMLGVGDFYYELGVQIIEVCLALKHRNGGLITLEELR-QQVLKGRGKFAQ
          .CA...GVD.L.SG.KGFWSE...VG.FY.ELG...IEVC.A.K.RNGG..TLEELR.Q..LKGRG.FAQ
Retrocopy TCA<PLGVDRLPSG<KGFWSETVSVGAFYCELGIRMIEVCVAPKLRNGGPLTLEELR<QHALKGRGRFAQ

Parental  DVSQDDLLRAIKKLKALGSGFG-IIPVGGTYLIQSVPAELNMDHTVVLQLA-EKNGYVTVSDIKASLKWE
          D..QDD..RA..KLKALG.GF...I.VGG...IQ..PAEL..D..VV.QLA..KNGYVTVSD.KA.LKWE
Retrocopy DAGQDDSIRAMEKLKALGTGFA<VISVGGAQRIQRAPAELKADPPVVQQLA<GKNGYVTVSDSKARLKWE

Parental  TE
          ..
Retrocopy AK

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_164 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_164 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005062	1 retrocopy	retro_amel_164 ,
Canis familiaris	ENSCAFG00000016893	1 retrocopy	retro_cfam_1488,
Choloepus hoffmanni	ENSCHOG00000013760	1 retrocopy	retro_chof_1372,
Callithrix jacchus	ENSCJAG00000007322	2 retrocopies	retro_cjac_1175, retro_cjac_1922,
Echinops telfairi	ENSETEG00000000758	1 retrocopy	retro_etel_709,
Felis catus	ENSFCAG00000008944	2 retrocopies	retro_fcat_1291, retro_fcat_574,
Homo sapiens	ENSG00000159210	1 retrocopy	retro_hsap_2394,
Gorilla gorilla	ENSGGOG00000025290	1 retrocopy	retro_ggor_1816,
Macropus eugenii	ENSMEUG00000016638	1 retrocopy	retro_meug_663,
Mustela putorius furo	ENSMPUG00000015356	1 retrocopy	retro_mputfur_1425,
Mus musculus	ENSMUSG00000006058	1 retrocopy	retro_mmus_1050,
Nomascus leucogenys	ENSNLEG00000002743	1 retrocopy	retro_nleu_2520,
Oryctolagus cuniculus	ENSOCUG00000009156	2 retrocopies	retro_ocun_814, retro_ocun_996,
Pongo abelii	ENSPPYG00000008911	1 retrocopy	retro_pabe_2161,
Tarsius syrichta	ENSTSYG00000004576	1 retrocopy	retro_tsyr_843,