RetrogeneDB ID: retro_pvam_1170

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_3593:104813..104996(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSPVAG00000009036
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_pvam_1170
TGGCGAATGGAGTACAAAGGCAATCTGGTATCTGTAGATGGCTATATGAACATGCAGCTTGCAAACCCAGAAGAATACAT
AAATGGAGCATTGCCTGGAGATCTGCGTAAAGTTTTAACAAGTTGTAATAATGTCCTTTATATCAGTGTTGAAGAAGAGG
AAAAAGATAGGAAAATAAGAGAA

Alignment

ORF - retro_pvam_1170 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 72.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WGMEYKGYLVSVDGYMNMQLANTEEYIDGALSGHLGEVLIRCNNVLYIRGVEEEEEDGEMRE
          W.MEYKG.LVSVDGYMNMQLAN.EEYI.GAL.G.L..VL..CNNVLYI..VEEEE.D...RE
Retrocopy WRMEYKGNLVSVDGYMNMQLANPEEYINGALPGDLRKVLTSCNNVLYI-SVEEEEKDRKIRE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_1170 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus 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 14 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Bos taurus	ENSBTAG00000016271	1 retrocopy	retro_btau_765,
Equus caballus	ENSECAG00000019817	1 retrocopy	retro_ecab_154,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Homo sapiens	ENSG00000139343	3 retrocopies	retro_hsap_125, retro_hsap_2487, retro_hsap_2645,
Gorilla gorilla	ENSGGOG00000001127	2 retrocopies	retro_ggor_1549, retro_ggor_225,
Macaca mulatta	ENSMMUG00000009302	4 retrocopies	retro_mmul_1521, retro_mmul_361, retro_mmul_550, retro_mmul_893,
Mustela putorius furo	ENSMPUG00000007176	3 retrocopies	retro_mputfur_1309, retro_mputfur_377, retro_mputfur_941,
Mus musculus	ENSMUSG00000020018	4 retrocopies	retro_mmus_1060, retro_mmus_1197, retro_mmus_2537, retro_mmus_3210,
Nomascus leucogenys	ENSNLEG00000005835	3 retrocopies	retro_nleu_2259, retro_nleu_274, retro_nleu_651,
Pongo abelii	ENSPPYG00000004847	2 retrocopies	retro_pabe_381, retro_pabe_489,
Pteropus vampyrus	ENSPVAG00000009036	1 retrocopy	retro_pvam_1170 ,
Rattus norvegicus	ENSRNOG00000005556	4 retrocopies	retro_rnor_1822, retro_rnor_1849, retro_rnor_2926, retro_rnor_444,
Sus scrofa	ENSSSCG00000000895	1 retrocopy	retro_sscr_958,