RetrogeneDB ID: retro_pvam_1282

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_5505:100942..101529(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSPVAG00000016032
• Aliases: None
• Description: nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]

Sequence

>retro_pvam_1282
GAACATGATGAACCAATTTTAAGCACTTGAAAACTATTAAAGTGAAGTTCTCAGATGCTGGCCAGTCTATAAGTTTTTTC
TTAGAATTTCACTTCGAACACAATGAATATTTCATAAATCAAATGCTGACAAAGATCTCTAGAGGACGAGGTCAGAACCA
ATGATTTTGTTCACTTTTCTTCTGATGGACCAGAAATTTATGGGTTGTACAGGGTGCCAGATAGATTGGAAAAAAGGGAA
GAATGTCACTTAGAAAACCACTAAGCAGCAGAAACACAAGAGACATGAGACAGTTCATACTGTGACCAAAACAGTTTCCA
ATAACTTTCTTTAATTTTTCTGCCTCTCCTTAAGTTCCTGAGTGTGGAGATCTGGATGATGCTGCTGAAGCTATCCTTGC
CGCAGACTTTGAAACTGGTCACTTTTTACATGAGCGTATAATCCCAAGATCAGTGTTATACTTTACCGGAGATGCTACTG
AAGATGATGATGATGATGATTATGAAGAAGGTGGAGAAGGAAATGAGGAAAATGATCCAGACTATGACTCAAAGAAAGAC
CAAAACCCAACAGAGTGTAAACAGCAG

Alignment

ORF - retro_pvam_1282 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.17 %
• Parental protein coverage: 50.26 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EHDEPIL-KHLKDIKVKFSDAGQPMSFVLEFHFEPNEYFTNEVLTKTYRMRSE-PDDSDPFSFDGPEI-M
          EHDEPIL.KHLK.IKVKFSDAGQ..SF.LEFHFE.NEYF.N..LTK..R.R.....D...FS.DGPEI.M
Retrocopy EHDEPIL<KHLKTIKVKFSDAGQSISFFLEFHFEHNEYFINQMLTKISRGRGQ>TNDFVHFSSDGPEI>M

Parental  GCTGCQIDWKKGKNVTLKTIKKKQKHKGRGTVRTVTKTVSNDSFFNFF-APPEVPESGDLDDDAEAILAA
          GCTGCQIDWKKGKNVT.KT..K.QKHK...TV.TVTKTVSN..F..FF.A.P.VPE.GDLDD.AEAILAA
Retrocopy GCTGCQIDWKKGKNVT*KT-TKQQKHKRHETVHTVTKTVSN-NFL*FF>ASP*VPECGDLDDAAEAILAA

Parental  DFEIGHFLRERIIPRSVLYFTGEAIEDDDDDYDEEGEEADEEGEEE-DEENDPDYDSKKDQ
          DFE.GHFL.ERIIPRSVLYFTG.A..........EG.E..EE.....D...D......K.Q
Retrocopy DFETGHFLHERIIPRSVLYFTGDAXXXXXXXXXXEGGEGNEENDPDYDSKKDQNPTECKQQ

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_1282 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 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pteropus vampyrus	ENSPVAG00000009190	1 retrocopy	retro_pvam_732,
Pteropus vampyrus	ENSPVAG00000016032	2 retrocopies	retro_pvam_1282 , retro_pvam_306,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Ictidomys tridecemlineatus	ENSSTOG00000003046	2 retrocopies	retro_itri_1007, retro_itri_416,