RetrogeneDB ID: retro_mmus_3206

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:62487240..62488489(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hspd1
• Ensembl ID: ENSMUSG00000025980
• Aliases: Hspd1, 60kDa, Hsp60
• Description: heat shock protein 1 (chaperonin) [Source:MGI Symbol;Acc:MGI:96242]

Sequence

>retro_mmus_3206
ATGCTTCGACTATCCACAGTCCTTCCCCAGATGAGACCAGTGTCCCATGCACTGGCTCCTAATCTCATTCAGGCCTAGGC
CAAAGATGTAAAATTTGGTGCAGGTGGTCAAACTTTAGTGTTTCAAGGTATAAACCTTTCAGCCAATGATGTAGCTGCTA
CAATGGGGCCAAAGAGAAGAACATTGATTATTGAACAGAGTCAGGGAAGTCCCAAAGTAACAAAAGGTGAGGTTACTGTC
ACAAAGCCAATTGATTTAAAGGATAAATGCAAAACTATCAGATCTAAACTTGTTCAGGGTGTTGCCAATAATACAAATGA
AGAGGCTGGGGATGGCACCACCACTGTCTCTGTTCTGGCACGCTCTATTGCCAATGACTTTGAGAAGATCAGCAAAGGGA
AAAATCCACTGGAAATCCGGAGAGGGGTGATGTTGGCTGTCAGTGCTGTAATTGCTCAACTTAAGAAACGATCTAAACCT
GTGACAACCCCTGAAGAAATTACCCAGATTGCTACAATTTCTGCAAATAGAGGCAAAGACTTTGGGAACATCATTTCTGA
TGCAATGAGAAAAGGTTGGAAGAAATGGTGTCATCACAGTGAGGGATGGAAAAACCCTGAATGATGAGCTAGAAATTATT
GAAGACATGAAGTTTGATAGAGGATATAATCCCCCATATTTTATTAACATGTCAAAAGGTCAAAAGTGTGAATTCCAAGA
TGCCTATGTTTTGTTGAGTGAAAAGAAAATGTCTAGTGTTCCGTCCATTGTACCTGCTCTTGAAATTGCTAATGCTCATC
AGAAGCCTTGGTCATAATTGCTGAAGATGGTGACAGAGAAACTTTAAGGACATTGGTTTTGAACAGGCTAACAGTTGGTC
TTCAAGTTGTAGCAGTCAAAGCTCCAGGGTTTGGGGACAATAGGAAGAACCAGCTTAAAAATATGGCTATTGCTAGTGGT
GGTGTGGTGTTTGGAGAAAAGGGGTTGAATATGAATCTTGAAGATGTTCAAGCTCATGACTTAGGAAAAGTTTTAGAGGT
CATTGTCACCAAAAATGGTGCCATGCTTTTGAAAGGAAAAGGTGACAAAGCTCACATTGAAAAATATATTCAAAATCACT
GAGCAGCTAGACATCACAAGTGAATATGAAAAGGAAAAGCTGAACGAGTGACTTGCTAAACTTTCAGATGAAGTACCTGT
GCTAAACCTTGGAGGGACAAGTGATGTGGAAGTGAATGAGAAGAATGAC

Alignment

ORF - retro_mmus_3206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.91 %
• Parental protein coverage: 73.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MLRLPTVLRQMRPVSRALAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGRTVIIEQSWGS
          MLRL.TVL.QMRPVS.ALAP.L..A.AKDVKFGA....L..QG..L.A..VA.TMGPK.RT.IIEQS.GS
Retrocopy MLRLSTVLPQMRPVSHALAPNLIQA*AKDVKFGAGGQTLVFQGINLSANDVAATMGPKRRTLIIEQSQGS

Parental  PKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVEI
          PKVTK..VTV.K.IDLKDK.K.I..KLVQ.VANNTNEEAGDGTTT..VLARSIA...FEKISKG.NP.EI
Retrocopy PKVTKGEVTVTKPIDLKDKCKTIRSKLVQGVANNTNEEAGDGTTTVSVLARSIAND-FEKISKGKNPLEI

Parental  RRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKDIGNIISDAMKK-VGRKGVITVKDGKTLND
          RRGVMLAV.AVIA.LKK.SKPVTTPEEI.Q.ATISAN..KD.GNIISDAM.K.VGR.GVITV.DGKTLND
Retrocopy RRGVMLAVSAVIAQLKKRSKPVTTPEEITQIATISANRGKDFGNIISDAMRK>VGRNGVITVRDGKTLND

Parental  ELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSIVPALEIANAHRKP-LVIIAEDV
          ELEIIE.MKFDRGY..PYFIN.SKGQKCEFQDAYVLLSEKK.SSV.SIVPALEIANAH.KP.LVIIAED.
Retrocopy ELEIIEDMKFDRGYNPPYFINMSKGQKCEFQDAYVLLSEKKMSSVPSIVPALEIANAHQKP<LVIIAEDG

Parental  DGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLNLNLEDVQAHDLGKVGEV
          D.E.L.TLVLNRL.VGLQVVAVKAPGFGDNRKNQLK.MAIA.GG.VFGE.GLN.NLEDVQAHDLGKV.EV
Retrocopy DRETLRTLVLNRLTVGLQVVAVKAPGFGDNRKNQLKNMAIASGGVVFGEKGLNMNLEDVQAHDLGKVLEV

Parental  IVTKDDAMLL-KGKGDKAHIEKRIQEITEQLDITTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEK
          IVTK..AMLL.K.K..K....K.I..ITEQLDI.TSEYEKEKLNE.LAKLSD.V.VL..GGTSDVEVNEK
Retrocopy IVTKNGAMLL>KEKVTKLTL-KNIFKITEQLDI-TSEYEKEKLNE*LAKLSDEVPVLNLGGTSDVEVNEK

Parental  KD
          .D
Retrocopy ND

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	0.00 RPM	93.17 RPM
SRP007412_cerebellum	0.00 RPM	79.33 RPM
SRP007412_heart	0.00 RPM	210.75 RPM
SRP007412_kidney	0.02 RPM	298.39 RPM
SRP007412_liver	0.00 RPM	313.50 RPM
SRP007412_testis	0.00 RPM	22.73 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3206 was not detected

EST

No EST(s) were mapped for retro_mmus_3206 retrocopy.

TSS

No TSS is located nearby retro_mmus_3206 retrocopy 5' end.

Lab

retro_mmus_3206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3206 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013770	1 retrocopy	retro_amel_771,
Canis familiaris	ENSCAFG00000010865	4 retrocopies	retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus	ENSCJAG00000003990	6 retrocopies	retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi	ENSETEG00000009184	4 retrocopies	retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens	ENSG00000144381	7 retrocopies	retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930, retro_hsap_4018,
Gorilla gorilla	ENSGGOG00000008267	6 retrocopies	retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana	ENSLAFG00000000053	1 retrocopy	retro_lafr_476,
Macropus eugenii	ENSMEUG00000011987	2 retrocopies	retro_meug_1688, retro_meug_224,
Myotis lucifugus	ENSMLUG00000000871	4 retrocopies	retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta	ENSMMUG00000010489	1 retrocopy	retro_mmul_83,
Monodelphis domestica	ENSMODG00000012289	3 retrocopies	retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furo	ENSMPUG00000007818	3 retrocopies	retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus	ENSMUSG00000025980	5 retrocopies	retro_mmus_1225, retro_mmus_2494, retro_mmus_3206 , retro_mmus_439, retro_mmus_706,
Nomascus leucogenys	ENSNLEG00000006874	7 retrocopies	retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii	ENSOGAG00000034053	5 retrocopies	retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii	ENSPPYG00000013046	5 retrocopies	retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Rattus norvegicus	ENSRNOG00000014525	9 retrocopies	retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Xenopus tropicalis	ENSXETG00000007509	1 retrocopy	retro_xtro_63,