RetrogeneDB ID: retro_pvam_180

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_1760:272435..272927(+)
• Located in intron of: ENSPVAG00000008040

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS24
• Ensembl ID: ENSPVAG00000015911
• Aliases: None
• Description: mitochondrial ribosomal protein S24 [Source:HGNC Symbol;Acc:14510]

Sequence

>retro_pvam_180
ATGGAGGCGCCCATGTGCAGCAGGGGGCTCAGGCTGTGGGTGCTGTCCTAGAGCCGAGAACTGCTATGTACCTGGCACAC
CCTGCATACCTCTGCAGTCTGTGCCAAGAATCAGGTGGCCCAAGTCCAAGTGGGCAAGGGGGACAAGCAAGTGACCTACG
AGGAGGCACACGCACACCACCACATAGCCCACCGCAAGGGCTGGCTGGCTGTGCACACAGGTACCTAGATGGGGAGGACC
ATGCTGCAGAGTGAACAGTGGAGGATGTTTTTCTTCTCAAGTTCATGCTGGGCACCTTCCCAGGCTGCCTGGCTGACCAG
CTTATCCTAAAGCGCTGGGCTAACTAGGTGGACAGCTGTGCTCTGATCCTGAGGCAGCTGCTTGCACACAAGTCCTAATT
CCTCAATGGGCTACAGTAAGATTCTGCTGTCCCACTTCTACAAGTGTCCTGTGCATCTGCCCCTCCAAATTGTGCCCTCA
AAGGTTGTGTAT

Alignment

ORF - retro_pvam_180 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.9 %
• Parental protein coverage: 98.2 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPVFSRGLGPRVLSWGRELPCPWRTLHTSAICAKNRAARVRVGKGDKPVSYEEAHAPHHIAHRKGWLS
          M.AP..SRGL...VLS..REL.C.W.TLHTSA.CAKN..A.V.VGKGDK.V.YEEAHA.HHIAHRKGWL.
Retrocopy MEAPMCSRGLRLWVLS*SRELLCTWHTLHTSAVCAKNQVAQVQVGKGDKQVTYEEAHAHHHIAHRKGWLA

Parental  LHTGN-LDGEDHAAERTVEDVFLRKFMLGTFPGCLADQLIIKRRANQVDICALVLRQLPVHKSYFL-VGY
          .HTG..LDGEDHAAE.TVEDVFL.KFMLGTFPGCLADQLI.KR.AN.VD.CAL.LRQL..HKS.FL..GY
Retrocopy VHTGT<LDGEDHAAE*TVEDVFLLKFMLGTFPGCLADQLILKRWAN*VDSCALILRQLLAHKS*FL>MGY

Parental  SETLLSHFYKCPVRLHLQTVPSKVVY
          S..LLSHFYKCPV.L.LQ.VPSKVVY
Retrocopy SKILLSHFYKCPVHLPLQIVPSKVVY

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_180 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017491	1 retrocopy	retro_amel_1126,
Bos taurus	ENSBTAG00000007398	1 retrocopy	retro_btau_411,
Choloepus hoffmanni	ENSCHOG00000003106	1 retrocopy	retro_chof_2334,
Dasypus novemcinctus	ENSDNOG00000016853	3 retrocopies	retro_dnov_1195, retro_dnov_153, retro_dnov_2049,
Echinops telfairi	ENSETEG00000016782	1 retrocopy	retro_etel_1350,
Homo sapiens	ENSG00000062582	1 retrocopy	retro_hsap_836,
Gorilla gorilla	ENSGGOG00000005692	1 retrocopy	retro_ggor_687,
Loxodonta africana	ENSLAFG00000011905	1 retrocopy	retro_lafr_426,
Macaca mulatta	ENSMMUG00000002405	1 retrocopy	retro_mmul_1089,
Monodelphis domestica	ENSMODG00000013889	1 retrocopy	retro_mdom_1785,
Pan troglodytes	ENSPTRG00000019127	1 retrocopy	retro_ptro_583,
Pteropus vampyrus	ENSPVAG00000015911	4 retrocopies	retro_pvam_1129, retro_pvam_1360, retro_pvam_180 , retro_pvam_978,
Tursiops truncatus	ENSTTRG00000002938	1 retrocopy	retro_ttru_1860,