RetrogeneDB ID: retro_mmus_1299

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 14:92602559..92604388(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hspa5
• Ensembl ID: ENSMUSG00000026864
• Aliases: Hspa5, AL022860, AU019543, Bip, D2Wsu141e, D2Wsu17e, Grp78, Hsce70, SEZ-7, Sez7, baffled, mBiP
• Description: heat shock protein 5 [Source:MGI Symbol;Acc:MGI:95835]

Sequence

>retro_mmus_1299
GGACCTGCAGTTGGCATTGATCTTGGGACCACCTACTCCTGTGTGGGTGTCTTCCATCATGGAAAGGTGGAAATTATTGC
CAATGACCAGGGTAACCGCACCGCGCCGAGCTACGTTGCTTTCACCGGCACAGAGAGATTAATTCAGGATGCGGCCAAGA
ATCAGGTTGCAAAGAACCCCACCAACACAGTTTTTGATGCCAAACGTCTGGTCGGGCGTAGGTTTGATGATGCTGTTGTT
CAGTCTGATATGAAGCACTGGCCCTTCATGGTGGTGAATGATGCAGGCAGGCCCAAGGTCCAAGTGGAATACAAAGGGGA
GACAACAAGTTTCTACCCAGAGAAAGTGTCCTCCACGGTTCTGACAAAGATGAAGGAAATTGCAGAAGCGTACCTCGGAA
AGACTGTTATCAATGCTGTGGTCACAGTGCCGGCTTACTTCAATGACTCTCAGCGACAGGCAACAAAAGATGCTGGAACT
ATTGCTGGCCTCAATGTACTTCGAATCATCAATGAACCAACTGCTGCTGCTATTGCTTATGGCTTAGATAAGAAGGTTGG
AGCTGAAAGGAATGTGCTCATTTTTGACTTGGGAGGTGGCACTTTTGATGTGTCAATCCTGACTATTGAGGATGGAAGTT
TTGAAGTCAAATCAACAGCTGGAGACACCCACTTAGGTGGAGAAAGTTTTGACAACCGAATGGTCAATCATTTCATTGCT
GAGTTTAAGCGAAAGCACAAGGAAGATGTCAGTGAGAACAAGAGAGCTGTCCGCCGTCTCCGCACCGCCTGCGAGCCAAG
CGCACCCTTTCCTCCAGCACCCAGGCCAGTATTGAGATTGATTCTCTCTATGAGGGAATTGACTTCTATACCTCCATTAC
CCGGGCTCGATTTGAGGAGTTGAATGCTGACCTGTTCCGTGGCCCACTGGACCCTGTAGAGAAAGCCCTTCGAGATGCCA
AACTGGACAAGTCACAGATCCATGATATTGTCTTGGTGGGTGGTTCTACCAGAATCCCCAAGATTCAGAAATTTCTGCAA
GACTTCTTCAATGGAAAAGAGCTGAACAAGAGCATTAACCCCGATGAAGCTGTTGCCTATGGTGCAGCTGTCCAGGCAGC
CATTCTATCTGGAGACAAGTCTGAGAACGTTCAGGATTTGCTGCTCTTGGATGTCACTCCTCTTTCCCTTGGTATTGAAA
CTGCTGGCAGAGTCATGACTGTCCTCATCAAGTGCAATACCACCATCCCTACCAAGCAGACACAGACTTTCACCACCTAC
TCTGACAACCAGCCTGGTGTACTCATTCAGGTGTATGAAGGTGAAAGGGCCATGACCAAGGACAACAACCTGCTTGGAAA
GTTCGAGCTCACGGGCATCCCTCCAGCACCCCGTGGGGTTCCTCAGATTGAGGTTACTTTTGACATCGATGCCAATGGCA
TCCTCAATGTTTCTGCTGTAGTTAAGAGCACAGGAAAGAAGAAAAAGATCACCATCACCAATGACAGGGGCCACTTGAGT
AAGGAAGATATTGAGCGCATGGTCCAAGAAGCTGAAAAGTACAAAGCTGAGGATGAGAAGCAGAGAGATAAAGTTTCCTC
CAAGAATTCACTGGAGTCCTATGCCTTCAACATGAAAGCAACTGTGGAAGATGAGAAACTTCAAGGCAAGATCAATGATA
AAGACAAGCAGATTCTTGACAAGTGCAATGAAATCATCAGCTGGCTGGATAAGAACCAGACTGCAGAGAAGGAAGAATTT
GAGCATCAGCAGAAAGAACTGGAGAAAGTCTGCAACCCTATCATTACCAAGCTGTACCAGAGTGCTGGT

Alignment

ORF - retro_mmus_1299 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.66 %
• Parental protein coverage: 93.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTPEGERLIGDAAKNQLTSNPENTVFDAKR
          G..VGIDLGTTYSCVGVF..G.VEIIANDQGNR..PSYVAFT...ERLI.DAAKNQ...NP.NTVFDAKR
Retrocopy GPAVGIDLGTTYSCVGVFHHGKVEIIANDQGNRTAPSYVAFTGT-ERLIQDAAKNQVAKNPTNTVFDAKR

Parental  LIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTFAPEEISAMVLTKMKETAEAYLGKKVTH
          L.GR...D..VQ.D.K..PF.VV.....P..QV...G..T..F.PE..S..VLTKMKE.AEAYLGK.V..
Retrocopy LVGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKG-ETTSFYPEKVSSTVLTKMKEIAEAYLGKTVIN

Parental  AVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLDKREG-EKNILVFDLGGGTFDVSLLT
          AVVTVPAYFND.QRQATKDAGTIAGLNV.RIINEPTAAAIAYGLDK..G.E.N.L.FDLGGGTFDVS.LT
Retrocopy AVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSILT

Parental  IDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVRKDNRAVQKLRREV-EKAKRALSSQHQA
          I..G.FEV..T.GDTHLGGE.FD.R...HFI....K...K.....N.......R.....AKR.LSS..QA
Retrocopy IEDGSFEVKSTAGDTHLGGESFDNRMVNHFIAEF-KRKHKEDVSENKRAVRRLRTA<LRAKRTLSSSTQA

Parental  RIEIESFFEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDSDLKKSDIDEIVLVGGSTRIPKIQQLV
          .IEI.S..EG.DF....TRA.FEELN.DLFR....PV.K.L.D..L.KS.I..IVLVGGSTRIPKIQ...
Retrocopy SIEIDSLYEGIDFYTSITRARFEELNADLFRGPLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKFL

Parental  KEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGD--QDTGDLVLLDVCPLTLGIETVGGVMTKLIPRNTVV
          ..FFNGKE....INPDEAVAYGAAVQA..LSGD......DL.LLDV.PL.LGIET.G.VMT.LI..NT..
Retrocopy QDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGRVMTVLIKCNTTI

Parental  PTKKSQIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIPPAPRGVPQIEVTFEIDVNGILRVTA
          PTK..Q.F.T.SDNQP.V.I.VYEGER..TKDN.LLG.F.LTGIPPAPRGVPQIEVTF.ID.NGIL.V.A
Retrocopy PTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVSA

Parental  EDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKKLKERIDTRNELESYAYSLKNQIGDKEKLG
          ..K.TG.K.KITITND...L..E.IERMV..AEK...ED.K........N.LESYA...K....D.EKL.
Retrocopy VVKSTGKKKKITITNDRGHLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVED-EKLQ

Parental  GKLSSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQPIISKLYGSGG
          GK....DK....K...E.I.WL...Q.A..E.F....KELE....PII.KLY.S.G
Retrocopy GKINDKDKQILDKC-NEIISWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAG

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	1.07 RPM	254.63 RPM
SRP007412_cerebellum	2.26 RPM	314.11 RPM
SRP007412_heart	0.40 RPM	480.28 RPM
SRP007412_kidney	2.60 RPM	534.24 RPM
SRP007412_liver	1.64 RPM	808.28 RPM
SRP007412_testis	0.32 RPM	401.86 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1299 was not detected

EST

No EST(s) were mapped for retro_mmus_1299 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_38107	44 libraries	37 libraries	395 libraries	229 libraries	367 libraries

The graphical summary, for retro_mmus_1299 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1299 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1299 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006880	1 retrocopy	retro_cjac_2221,
Homo sapiens	ENSG00000044574	1 retrocopy	retro_hsap_3005,
Gallus gallus	ENSGALG00000001000	1 retrocopy	retro_ggal_21,
Gorilla gorilla	ENSGGOG00000026879	1 retrocopy	retro_ggor_2082,
Macropus eugenii	ENSMEUG00000016702	1 retrocopy	retro_meug_522,
Mus musculus	ENSMUSG00000015656	8 retrocopies	retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Mus musculus	ENSMUSG00000024359	1 retrocopy	retro_mmus_3624,
Mus musculus	ENSMUSG00000026864	1 retrocopy	retro_mmus_1299 ,
Nomascus leucogenys	ENSNLEG00000017348	1 retrocopy	retro_nleu_751,
Otolemur garnettii	ENSOGAG00000006786	1 retrocopy	retro_ogar_2901,
Pongo abelii	ENSPPYG00000019609	1 retrocopy	retro_pabe_2491,
Pan troglodytes	ENSPTRG00000000563	1 retrocopy	retro_ptro_2033,
Ictidomys tridecemlineatus	ENSSTOG00000011243	4 retrocopies	retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,