RetrogeneDB ID: retro_pvam_133

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1557:16771..17288(-)
• Located in intron of: ENSPVAG00000012536

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18A
• Ensembl ID: ENSPVAG00000017378
• Aliases: None
• Description: ribosomal protein L18a [Source:HGNC Symbol;Acc:10311]

Sequence

>retro_pvam_133
ATGAAGGCCTCCTGCGCGCTGTGAGAACACAGGTTGTGGGGCGCTGCCTGCCCACCCCCAAGTGCTACCCGCCGCCCCTC
TGCCGCATGCGCATCTTCGCGCCTAACCATGTGACCAAGTCTCGCTTCTGGTATTTTGTGTCTCAGCCGAAGATGAAGAA
GTCTTCAGGGGAAATTGTCTGCTATGGGCAGATGTTCGATAAATCCCCGTGGGTGAAGAACTTTATTATCTGGCTGCACT
ACGACTCCCGGAGCAGCACCCACAGCATATACAAGAAATAACGTGACCTGACTGCTGCAGGCGCAGTCACCCAGTGCTCC
CGAGACCTGGGGGCCAGGCACCTTGCCGGTGCCCACCCAATCCAGATCAGGAAGTTGGAGGAGATTGCAGCCAGCAAGTG
CTGCCACCGGAAGTTGAGCAGTTTCACGACTCCAGGGTCAAGTTCTCGCTTCGCCACTGGGTCCTTCATCACTAGCACAA
GCCACGCTTCACCATCAACAGGCCTAACACCCTCTTT

Alignment

ORF - retro_pvam_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.35 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKASGTLREYK-VVGRCLPTPKCRTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFE
          MKAS..L.E...VVGRCLPTPKC..PPL.RMRIFAPNHV..KSRFWYFVSQ..KMKKSSGEIV..GQ.F.
Retrocopy MKASCAL*EHR<VVGRCLPTPKCYPPPLCRMRIFAPNHVT-KSRFWYFVSQ-PKMKKSSGEIVCYGQMFD

Parental  KSPLRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRR
          KSP..VKNF.IWL.YDSRS.TH..Y...RDLT.AGAVTQC.RD.GARH.A.AH.IQI.K.EEIAASKC..
Retrocopy KSPW-VKNFIIWLHYDSRSSTHSIYKK*RDLTAAGAVTQCSRDLGARHLAGAHPIQIRKLEEIAASKCCH

Parental  -PAVKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF
          .P.V.QFHDS..KF.L.H.VL...HKPRFT..RPNT.F
Retrocopy <PEVEQFHDSRVKFSLRHWVLHH*HKPRFTINRPNTLF

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_133 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 18 parental genes, and 70 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003125	1 retrocopy	retro_acar_86,
Bos taurus	ENSBTAG00000015831	5 retrocopies	retro_btau_145, retro_btau_1586, retro_btau_842, retro_btau_917, retro_btau_922,
Canis familiaris	ENSCAFG00000015122	1 retrocopy	retro_cfam_231,
Callithrix jacchus	ENSCJAG00000014006	7 retrocopies	retro_cjac_1628, retro_cjac_2814, retro_cjac_3192, retro_cjac_3906, retro_cjac_4134, retro_cjac_441, retro_cjac_642,
Cavia porcellus	ENSCPOG00000015205	1 retrocopy	retro_cpor_1478,
Equus caballus	ENSECAG00000015258	1 retrocopy	retro_ecab_745,
Felis catus	ENSFCAG00000007518	6 retrocopies	retro_fcat_1190, retro_fcat_1213, retro_fcat_1716, retro_fcat_1848, retro_fcat_267, retro_fcat_831,
Gorilla gorilla	ENSGGOG00000002870	8 retrocopies	retro_ggor_1215, retro_ggor_1680, retro_ggor_1868, retro_ggor_1933, retro_ggor_195, retro_ggor_227, retro_ggor_2775, retro_ggor_2940,
Macropus eugenii	ENSMEUG00000003228	2 retrocopies	retro_meug_36, retro_meug_49,
Macaca mulatta	ENSMMUG00000028844	6 retrocopies	retro_mmul_1416, retro_mmul_1591, retro_mmul_2233, retro_mmul_2547, retro_mmul_292, retro_mmul_364,
Monodelphis domestica	ENSMODG00000019167	2 retrocopies	retro_mdom_349, retro_mdom_680,
Mustela putorius furo	ENSMPUG00000015786	4 retrocopies	retro_mputfur_1007, retro_mputfur_1189, retro_mputfur_1574, retro_mputfur_457,
Pongo abelii	ENSPPYG00000009725	10 retrocopies	retro_pabe_1200, retro_pabe_1319, retro_pabe_1620, retro_pabe_2239, retro_pabe_2302, retro_pabe_3680, retro_pabe_3717, retro_pabe_3802, retro_pabe_482, retro_pabe_487,
Pan troglodytes	ENSPTRG00000010686	3 retrocopies	retro_ptro_1078, retro_ptro_1803, retro_ptro_27,
Pteropus vampyrus	ENSPVAG00000017378	6 retrocopies	retro_pvam_1314, retro_pvam_133 , retro_pvam_155, retro_pvam_200, retro_pvam_607, retro_pvam_828,
Sarcophilus harrisii	ENSSHAG00000000406	3 retrocopies	retro_shar_435, retro_shar_474, retro_shar_706,
Sus scrofa	ENSSSCG00000013889	2 retrocopies	retro_sscr_1103, retro_sscr_184,
Tursiops truncatus	ENSTTRG00000008977	2 retrocopies	retro_ttru_151, retro_ttru_508,