RetrogeneDB ID: retro_pvam_296

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_2403:262667..263157(+)
• Located in intron of: ENSPVAG00000009607

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNPS1
• Ensembl ID: ENSPVAG00000005105
• Aliases: None
• Description: RNA binding protein S1, serine-rich domain [Source:HGNC Symbol;Acc:10080]

Sequence

>retro_pvam_296
TCCAAGAAAATAAGAAGGCCAGCATTAGCATTTACCAAACACAAAGACCGTTCTGTTGAGAAGTTCAAGGATCGCTCTAA
AGATAAAGGGGCCACCAAGGAGTCGAGCAAGAACAATCGTGGCAGGGATAAAACTCTAAAGAGGCATAGCGCTTAGAGTG
GTAGCAGCAGCACCAGGTCTCGGTCCAGCTCTACCTCAAGCTCGGGCTTCAGCAAAAGCACCAGCACCAGCGAGCAGTAG
CTCTAGCTCCTCATCAACATCAAGCCGCTTGGGAAGTTCCAGCACATCCCACAGCTCCAGCTCCAGCAGCTCTTCTGGCT
CTCCGAGTCCTTCTCAGTGCAGACATGACAACAGGCAGTGTTACCTTCTCAGTGCAGACATGACCAAACCACCCAAAAGA
GATGAAGAGGAAAGGAAGAGGCGGAGCCCTTCACCTAAACCCACCAAAGTGCATATTGGAAGGCTCACCAGGAATGTGAC
CAAGGATCAC

Alignment

ORF - retro_pvam_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.61 %
• Parental protein coverage: 52.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NKKSSTRAPSPTKRKDRSDEKSKDRSKDKGATKETSEKDRGRDKTRKRRSASSGSSSTRSRSSSTSSSGS
          .KK....A...TK.KDRS.EK.KDRSKDKGATKE.S...RGRDKT.KR.SA.SGSSSTRSRSSSTSSSG.
Retrocopy SKKIRRPALAFTKHKDRSVEKFKDRSKDKGATKESSKNNRGRDKTLKRHSA*SGSSSTRSRSSSTSSSGF

Parental  STSTGSS-SGSSSSSA-SSRSGSSSTSRSSSSSSSSGSPSPSRRRHDNRR---RSRSKSKPPKRDEKERK
          S.ST..S.S.SSSSS..SSR.GSSSTS.SSSSSSSSGSPSPS..RHDNR.....S....KPPKRDE.ERK
Retrocopy SKSTSTS>SSSSSSSSTSSRLGSSSTSHSSSSSSSSGSPSPSQCRHDNRQCYLLSADMTKPPKRDEEERK

Parental  RRSPSPKPTKVHIGRLTRNVTKDH
          RRSPSPKPTKVHIGRLTRNVTKDH
Retrocopy RRSPSPKPTKVHIGRLTRNVTKDH

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_296 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 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004866	4 retrocopies	retro_chof_1587, retro_chof_1985, retro_chof_2272, retro_chof_493,
Cavia porcellus	ENSCPOG00000002066	2 retrocopies	retro_cpor_363, retro_cpor_953,
Equus caballus	ENSECAG00000023288	1 retrocopy	retro_ecab_524,
Gorilla gorilla	ENSGGOG00000014275	1 retrocopy	retro_ggor_2016,
Macropus eugenii	ENSMEUG00000008882	1 retrocopy	retro_meug_1996,
Monodelphis domestica	ENSMODG00000015891	1 retrocopy	retro_mdom_1171,
Otolemur garnettii	ENSOGAG00000031582	1 retrocopy	retro_ogar_3241,
Pan troglodytes	ENSPTRG00000031310	1 retrocopy	retro_ptro_1967,
Pteropus vampyrus	ENSPVAG00000005105	1 retrocopy	retro_pvam_296 ,
Rattus norvegicus	ENSRNOG00000008703	4 retrocopies	retro_rnor_1537, retro_rnor_2135, retro_rnor_2988, retro_rnor_649,
Sarcophilus harrisii	ENSSHAG00000016951	1 retrocopy	retro_shar_390,
Ictidomys tridecemlineatus	ENSSTOG00000013200	1 retrocopy	retro_itri_1160,