RetrogeneDB ID: retro_mmus_3507

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:112162553..112163744(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000083392
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Dnaja1
• Ensembl ID: ENSMUSG00000028410
• Aliases: Dnaja1, Hsj2, Nedd7
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:MGI Symbol;Acc:MGI:1270129]

Sequence

>retro_mmus_3507
ATGATGAAAGAAACCACTTACTACGATGTTTTGGGAGTCAAATCCAATGCCACCCAGGAACAATTGAAAAAGGCATATAG
AAAACTGGCCTTGAAGTACCACCCTGATAAGAATCCAAATGAAGGAGAAAAATTTAAACAGATTTCTGAAGCTTATGAAG
TTCTTGCTGATTCCAAAAAAAGGGAACTATATGATAAAGGAGGGGAGCAGGCGATTAAAGAGGGCGGAGCAGGTGGTGGT
TTTGGCTCACCCATGGATATCTTTGATATGTTCTTTGGAGGAGGAGGAAGAATGCAAAGAGAAAGGAGAGGTAAAAATGT
TGTTCATCACCTCTCAGTGACCTTAGAAGACTTATATAATGGTGCAACAAGAAAACTGGCTCTGCAAAAGAATGTGATTT
GTGACAAATGTGAAGGCCGAGGGGGTAAGAAAGGAGCAGTAGAGTGCTGTCCCAACTGCCAGGGGAAGGGCATGTAGATA
AGGATTCATCAGATTGGACCAGGAATGGTTCAGCAAATTCAGTCAGTGTGCATGGAGTGCCAGGGTCATGGAGAACGCAT
CAGTCCAAAAGACAGATGTAAAAGCTGCAATGGAAGAAAGATAGTTTGAGAGAAGAAAATTTTAGAAGTTTATATTGATA
AAGGCATGAAAGATGGTCAGAAGATAACATTCCACGGTGAAGGAGACCAAGAACCAGGACTTGAGCCAGGAGATATTATC
ATTGTGTTAGATCAGAAGGATCATGCCGTTTTTACAAGGCGAGGAGAAGACCTTTTCATGTGTATCGACATACAGCTGGT
TGAAGCATTGTGCGGCTTCCAAATGCCAGTATCTACTCTTGACAACCGAACCATTGTCATCACCTCTCATCCAGGTCAGA
CTGTCAAGTATGGGGATATAAAATGTGTGCTAAATGAAGGTATGCCAATATACTGTCGGCCATATGAAAAGGGACGTCTA
ATCATTGAGTTTAAGGTAAACTTTCCTGAAAATGGCTTTCTCTCTCCTGATAAACTCTCTTTGCTGGAAAAACTCCTTCC
TGAAAGGAAGGAAGTAGAAGAGACTGATGAAATGGATCAGGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGATGGC
GTCATTATAATGGAGAACCTTATGAGGATGATGAACGTCACCCCAGAGGTGGCGTCCAGTGTCAGACGTCT

Alignment

ORF - retro_mmus_3507 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.21 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVKETTYYDVLGVKPNATQEELKKAYRKLALKYHPDKNPNEGEKFKQISQAYEVLADSKKRELYDKGGEQ
          M.KETTYYDVLGVK.NATQE.LKKAYRKLALKYHPDKNPNEGEKFKQIS.AYEVLADSKKRELYDKGGEQ
Retrocopy MMKETTYYDVLGVKSNATQEQLKKAYRKLALKYHPDKNPNEGEKFKQISEAYEVLADSKKRELYDKGGEQ

Parental  AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHQLSVTLEDLYNGATRKLALQKNVICDKCEGR
          AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVH.LSVTLEDLYNGATRKLALQKNVICDKCEGR
Retrocopy AIKEGGAGGGFGSPMDIFDMFFGGGGRMQRERRGKNVVHHLSVTLEDLYNGATRKLALQKNVICDKCEGR

Parental  GGKKGAVECCPNCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEV
          GGKKGAVECCPNC.G.GM.IRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIV.EKKILEV
Retrocopy GGKKGAVECCPNCQGKGM*IRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIV*EKKILEV

Parental  HIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTL
          .IDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMC.DIQLVEALCGFQ.P.STL
Retrocopy YIDKGMKDGQKITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCIDIQLVEALCGFQMPVSTL

Parental  DNRTIVITSHPGQIVKHGDIKCVLNEGMPIYRRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
          DNRTIVITSHPGQ.VK.GDIKCVLNEGMPIY.RPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK
Retrocopy DNRTIVITSHPGQTVKYGDIKCVLNEGMPIYCRPYEKGRLIIEFKVNFPENGFLSPDKLSLLEKLLPERK

Parental  EVEETDEMDQVELVDFDPNQERRRHYNGEAYEDDEHHPRGGVQCQTS
          EVEETDEMDQVELVDFDPNQER.RHYNGE.YEDDE.HPRGGVQCQTS
Retrocopy EVEETDEMDQVELVDFDPNQERWRHYNGEPYEDDERHPRGGVQCQTS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.09 RPM	103.33 RPM
SRP007412_cerebellum	0.09 RPM	81.46 RPM
SRP007412_heart	0.00 RPM	33.68 RPM
SRP007412_kidney	0.17 RPM	125.45 RPM
SRP007412_liver	0.08 RPM	146.46 RPM
SRP007412_testis	0.05 RPM	69.93 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3507 was not detected

EST

No EST(s) were mapped for retro_mmus_3507 retrocopy.

TSS

No TSS is located nearby retro_mmus_3507 retrocopy 5' end.

Lab

retro_mmus_3507 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3507 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 83 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 ,
Mus musculus	ENSMUSG00000032285	1 retrocopy	retro_mmus_2632,
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,