RetrogeneDB ID: retro_pvam_605

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_4013:165157..165393(+)
• Located in intron of: ENSPVAG00000002525

Retrocopy information

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

Parental gene information

• Parental gene symbol: CKS2
• Ensembl ID: ENSPVAG00000011011
• Aliases: None
• Description: CDC28 protein kinase regulatory subunit 2 [Source:HGNC Symbol;Acc:2000]

Sequence

>retro_pvam_605
ATGGCCTACAAGCAGATCTACTACTCAGATCAAGTACCTCCTTGAGCACTATGAGTACTGAGATATCATGTTACCCAGAG
TACTTTTCAAACAAGTACCTCAAACCCATCTGATGTTTGAAGAGGAGTGGAAGAAATTTATTGTCCAAGAGTCTAGGATG
GGTTCATTACATTATTTATGAGCCAGAACCACATATTCTTCTCTTTAGATAACATCTTCCAAAAGATCAACAAAAA

Alignment

ORF - retro_pvam_605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.07 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAHKQIYYSD-KYFDEHYEYRHVMLPRELSKQVPKTHLMSEEEW-RRLGVQQSLGWVHYMIHEPEPHILL
          MA.KQIYYSD.KY..EHYEY...MLPR.L.KQVP.THLM.EEEW.R.L....SLGWVHY.I.EPEPHILL
Retrocopy MAYKQIYYSD>KYLLEHYEY*DIMLPRVLFKQVPQTHLMFEEEW>RNL-LSKSLGWVHYIIYEPEPHILL

Parental  FRRPLPKDQQK
          FR..LPKDQQK
Retrocopy FR*HLPKDQQK

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_605 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 13 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002194	2 retrocopies	retro_cfam_1495, retro_cfam_472,
Callithrix jacchus	ENSCJAG00000007792	1 retrocopy	retro_cjac_261,
Echinops telfairi	ENSETEG00000001260	10 retrocopies	retro_etel_1194, retro_etel_1752, retro_etel_1839, retro_etel_229, retro_etel_590, retro_etel_704, retro_etel_717, retro_etel_721, retro_etel_838, retro_etel_979,
Felis catus	ENSFCAG00000022286	1 retrocopy	retro_fcat_1875,
Macaca mulatta	ENSMMUG00000012534	1 retrocopy	retro_mmul_269,
Mus musculus	ENSMUSG00000062248	4 retrocopies	retro_mmus_1356, retro_mmus_1470, retro_mmus_2392, retro_mmus_409,
Nomascus leucogenys	ENSNLEG00000008729	1 retrocopy	retro_nleu_1793,
Otolemur garnettii	ENSOGAG00000028843	1 retrocopy	retro_ogar_798,
Pongo abelii	ENSPPYG00000025843	1 retrocopy	retro_pabe_57,
Pteropus vampyrus	ENSPVAG00000011011	3 retrocopies	retro_pvam_1297, retro_pvam_1307, retro_pvam_605 ,
Rattus norvegicus	ENSRNOG00000014130	5 retrocopies	retro_rnor_1209, retro_rnor_1909, retro_rnor_2742, retro_rnor_279, retro_rnor_402,
Sus scrofa	ENSSSCG00000021161	2 retrocopies	retro_sscr_458, retro_sscr_675,
Ictidomys tridecemlineatus	ENSSTOG00000000048	7 retrocopies	retro_itri_1058, retro_itri_1306, retro_itri_1429, retro_itri_1632, retro_itri_269, retro_itri_585, retro_itri_774,