RetrogeneDB ID: retro_pvam_672

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: GeneScaffold_647:10112..10903(+)
• Located in intron of: ENSPVAG00000010863

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSPVAG00000011470
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]

Sequence

>retro_pvam_672
ATTTGTGACAAATGTAAAGGCCAAGGTGGTAAGAAAGGAGCAGTACAATGCTGTCCTAATTGTCAAGGTACTGGGATGCA
AATCAGAATTCATCAGATAGGACCCAGAATGGTTCAGCAAATTCAGTCTATGTGCATGGAGTGCCGGTGCCATGAGAAAC
AGATCAGACCTAAAGACAGATGTAAAAACTACAATGGAAAGAAGATAGTTTGAGATAAGAAGATTCTAGAAGTTCATATG
GACAAAGGCATGAAAGATGGCCAGAAGATAACATTCCATGGTGAAAGAGACCAAGAACCAGGACTTGAGCGCAGAGATAT
TACCATAGTTTTAGATCAGAAAGACCATGCTGTTTTTACTTGACAAGAAGATCTTTTCATGTGTATGGACACAGAGCTGG
CTGAAGCATTGTGTGGCCTCCAAAAGTCAATATCTACTCTTGACAACCAAACCATAGTCATCACCTCTCATCCAGGTCAG
ATTGTCAAGCATGTAGATATCAAGTGTATGCTAAATGAAGGCATGCCATTTATTATAGAGCAAATGAAAAGGGTTGCCTA
ATCATCAAATTTAAGGCAAACTTTCCTAAGAATGACTTTCTTTCTCCTGCTAAACTCTCTTTGCTTGAAAACCTCCTACC
TGAAAGGAAGGAAGTAGAAGAGACTGATGAAATGGATCAGGTAGAACTGATGAATTTTGATCTAAGTCAAGAAAGACAGC
ACCATTACAATGGAGAAGCACATGAGTATGACGAACATCATGCTAGGGGTGGTGTTCAGGGTCAGACTTCT

Alignment

ORF - retro_pvam_672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.7 %
• Parental protein coverage: 66.58 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ICDKCEGRGGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIV
          ICDKC.G.GGKKGAV.CCPNC.GTGMQIRIHQIGP.MVQQIQS.CMEC..H...I.PKDRCK..NG.KIV
Retrocopy ICDKCKGQGGKKGAVQCCPNCQGTGMQIRIHQIGPRMVQQIQSMCMECRCHEKQIRPKDRCKNYNGKKIV

Parental  REKKILEVHIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCG
          ..KKILEVH.DKGMKDGQKITFHGE.DQEPGLE..DI.IVLDQKDHAVFT...EDLFMCMD..L.EALCG
Retrocopy *DKKILEVHMDKGMKDGQKITFHGERDQEPGLERRDITIVLDQKDHAVFT*Q-EDLFMCMDTELAEALCG

Parental  FQKPISTLDNRTIVITSHPGQIVKHGDIKCVLNEGMP-IYRRPYEKGRLIIEFKVNFPENGFLSPDKLSL
          .QK.ISTLDN.TIVITSHPGQIVKH.DIKC.LNEGMP.IY.R..EKG.LII.FK.NFP.N.FLSP.KLSL
Retrocopy LQKSISTLDNQTIVITSHPGQIVKHVDIKCMLNEGMP<IYYRANEKGCLIIKFKANFPKNDFLSPAKLSL

Parental  LEKLLPERKEVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
          LE.LLPERKEVEETDEMDQVEL..FD..QER..HYNGEA.E.DEHH.RGGVQ.QTS
Retrocopy LENLLPERKEVEETDEMDQVELMNFDLSQERQHHYNGEAHEYDEHHARGGVQGQTS

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_672 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 15 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Callithrix jacchus	ENSCJAG00000008022	10 retrocopies	retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus	ENSCPOG00000000462	6 retrocopies	retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus	ENSMLUG00000016086	7 retrocopies	retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mus musculus	ENSMUSG00000028410	3 retrocopies	retro_mmus_2561, retro_mmus_2982, retro_mmus_3507,
Procavia capensis	ENSPCAG00000012273	2 retrocopies	retro_pcap_184, retro_pcap_220,
Pteropus vampyrus	ENSPVAG00000011470	1 retrocopy	retro_pvam_672 ,
Rattus norvegicus	ENSRNOG00000007029	2 retrocopies	retro_rnor_2208, retro_rnor_608,
Sorex araneus	ENSSARG00000001373	5 retrocopies	retro_sara_280, retro_sara_312, retro_sara_671, retro_sara_741, retro_sara_748,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tarsius syrichta	ENSTSYG00000001329	4 retrocopies	retro_tsyr_110, retro_tsyr_1384, retro_tsyr_1921, retro_tsyr_57,