RetrogeneDB ID: retro_mmus_261

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:78664386..78666729(+)
• Located in intron of: ENSMUSG00000032883

Retrocopy information

• Ensembl ID: ENSMUSG00000079470
• Aliases: Utp14b, 4932411L21Rik, jsd
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Utp14a
• Ensembl ID: ENSMUSG00000063785
• Aliases: Utp14a, 2700066J21Rik, JsdX, NY-CO-16, SDCCAG16, T25628, mKIAA0266
• Description: UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast) [Source:MGI Symbol;Acc:MGI:1919804]

Sequence

>retro_mmus_261
ATGAAGCCAAAGATGAGACCAGATCCTTCTTCAAGAGCTAACAGGCCCTGTGAGAAGAAGGAGGCTGCTACCATGAACAT
GGCCAGGAATGTGACAGACCTTCTGGCTTTGAGCCAGCAGGAAGAACTAGTGGATTTGCCAGAAAACTATCCACTGAGTA
CGAGTGAAGATGAGGGGGACAGTGATGGAGAAGGAAAACGTCAAAAACTTCTGGAAGCAGTCAGTTCCCTTGGTAGAAAG
AATAAATGGAAGTTGGCAGAGAGATCTGAGGCTAGTCGGATGGTTTCAGAGTTCAATGTCACTTCTGAAGGATCAGGTGA
AAAGCTGGTCCTTTCCGATTTGCTTGGGTCTGCTACAGCATTATCTTCGGTGGCTGCTGTGAAAAAACAGCTGCATAGAG
TCAAGTCAAAGACGCTCACCCCACCCCTTAACAAAGAAGAGGCTGACCGAGCCCTCAGGGAAGCAGCATTCAGCAAAACC
TCACAAATGCTCTCCAGGTGGGATCCGGTGGTTCTGAAGAACCGGCAGGCAGAGCAGTTGATTTTTCCCATGGAGAAGGA
GCCGCCAGCGGTTGCACCCATTGAACATGTTTTTACTGACTGGAAAGTAAGAACCCCTCTGGAACGAGAAGTTTTTAACC
TTCTTCATAAGAACAAGCAGCCAGTAACAGACCCTTTATTGACTCCCGTGGAAACAGCCTCCATCAGAGCCATGAGCCTG
GAAGAAGCCAAGATACGCCGAGCAGAGCTTCAGAGGACGCGAGCTCTACAGTCCTATTATGAGGCTAGAGCTCGAAGAGA
GAAGAGAATCAAGAGTAAGAAGTATCACAGAGCTCTAAAGAAAGGAAAGGCCAAGAAAGCCTTAAAAGAGTTTGAAGAGC
TGTGGAAAGACTGCCCAAATGCTGCATTGCAAGAACTGGAGAAAATGGAAAAGGCCAGAATGACAGAACGGATGAGCCTT
AAGCACCAGGGCAGTGGGAAATGGGCAAAGTCAAAGGCAATTATGGCCAAATATGACCCTGAGGCTCGAAAAGCTATGCA
AGAACAATTGGCTAAGAACAGAGAACTGACACAGAAACTCCAGGTAGTTTCAGAGAGTGAGGAAGAGGACGGATGCACAG
AAGAGGGAATAGTCTCTGTCTCCCATGGAATGGATGACCTACAGATGAATGCAGATGGTGTAAATCCCTGGATGCTTAGC
AGTTGCAACAGCAATGCAAAGCGGGGTGAGATCAAGACCGATCCTGAACAGATGCCTGAGTTTGTGGCCCATGTGTCTTC
TGAGAGTGAGGGAGATGAAAGACCAGTGGCAGAAGAACTTGTGTTAAAAGAAAGATCCTTTCAAGAAAGAGTTGATCCCA
ACAATGCTAAGCTAATGGATGGCCAAGAAACAGAAGACTCTGATAGCCAGGAGGTATTACAGAAACTCAACAAGGAAAGT
CATCAATCTGACAATCAAAAAGTGAGTTCAGAGGAAAATGTTCTCCATATCCAGAGAGAGGACCTTGCCTCAGAGAAGTT
GTTGGTGCTTCAAAGGCTAGAGAGAGCACATGTTCTGGAACAACAAGGAGAGTTGAGCAAAGAAGAACATTATCCAAAAA
AAGGGCTTTCCAGACCTTTGTTGAAAGGGGATTGGAAGGAGATGAAGCCACTCACCAACCCTGATGCCTCTGGAGGGAAG
AAAAAGAAGGAACAAATGATTGATCTACGGAACCTCCTAACTGCTAACTCATCTCCTGTGAGGTCTTTGGCTGTGCCCAC
AATACAGCAGTTAGAAGATGAAGTGGAGACCGATCACAAGCAGCTAATAAGGGAAGCTTTTGCTGGGGATGATGTCATAA
GAGAGTTCTTAAAAGAGAAGAGGGAAGCTATAGAGACAAATAAACCAAAGGACTTGGACCTGTCATTGCCTGGATGGGGT
GAGTGGGTTGGTATGGGCCTGAAGCCCAGCGCCAAGAAAAGACGCCGTTTTCTTATTAAAGCTCCTGAGAGTTCTCCAAG
AAAAGACAAGAATTTGCCGAATGTGATTATCAGTGAGAAGCGCAACATCCATGCAGCTGCTCATCAGGTGCGGGCGCTTC
CACACCCATTCACCCACCAGCAGCAGTTTGAAAGGACTATCCAAAACCCTATTGGGTACATGTGGAACACCCAGAGGACC
TTCCAAAAGCTGACAGTTCCCAAGGTTGGCACCAAGCTAGGCCATATCATTAAGCCCATAAAAGCAGAAAATGTAGGGTA
CTGCTCTTCCACAAGGTCTGACCTCTCTATCCTACAGAGCAGTCAGAAGTGCCTCTCCAGAAAACAGCAAAAACAACTGA
AGAAGTTGAGCTCTGCAGATTGA

Alignment

ORF - retro_mmus_261 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.37 %
• Parental protein coverage: 61.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNSIKATKGLLALSQQDDLMDLTSNYPLSASEDEGDSDGERKHQKLLEAIGSLSGKNRWKLPERSEAGLK
          MN.......LLALSQQ..L.DL..NYPLS.SEDEGDSDGE.K.QKLLEA..SL..KN.WKL.ERSEA...
Retrocopy MNMARNVTDLLALSQQEELVDLPENYPLSTSEDEGDSDGEGKRQKLLEAVSSLGRKNKWKLAERSEASRM

Parental  VSEFNVSSEGSGEKLALSDLLGPLKPSSSLAAVKKQLSRVKSKKTLELPLHKREVEQIHREVAFSKTSQT
          VSEFNV.SEGSGEKL.LSDLLG.....SS.AAVKKQL.RVKSK.TL..PL.K.E.....RE.AFSKTSQ.
Retrocopy VSEFNVTSEGSGEKLVLSDLLGSATALSSVAAVKKQLHRVKSK-TLTPPLNKEEADRALREAAFSKTSQM

Parental  LSKWDSVVQKNREAEQLVFPLEKEPSSFAPMEHVFREWKARTPLEQEVFNLLHKNKQPVTDPLLTPVEKA
          LS.WD.VV.KNR.AEQL.FP.EKEP...AP.EHVF..WK.RTPLE.EVFNLLHKNKQPVTDPLLTPVE.A
Retrocopy LSRWDPVVLKNRQAEQLIFPMEKEPPAVAPIEHVFTDWKVRTPLEREVFNLLHKNKQPVTDPLLTPVETA

Parental  SLKAMSLEEAKIRRAELQRARALQSYYEARARRMKKIKSKKYHKIVKKGKAKKALKDFEQLRKVDPDAAL
          S..AMSLEEAKIRRAELQR.RALQSYYEARARR.K.IKSKKYH...KKGKAKKALK.FE.L.K..P.AAL
Retrocopy SIRAMSLEEAKIRRAELQRTRALQSYYEARARREKRIKSKKYHRALKKGKAKKALKEFEELWKDCPNAAL

Parental  EELEKMEKARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAMQEQLAKNKELTQKLQVVSESEEEGGAD
          .ELEKMEKARM.ERMSLKHQ.SGKWAKSKAIMAKYD.EAR.AMQEQLAKN.ELTQKLQVVSESEEE.G..
Retrocopy QELEKMEKARMTERMSLKHQGSGKWAKSKAIMAKYDPEARKAMQEQLAKNRELTQKLQVVSESEEEDGCT

Parental  EEEAL-VPDIVNEVQKTADGPNPWMLRSCSRDAKENEIQADSEQLPESAAHEFPENEENDKPVAEEDELL
          EE....V.......Q..ADG.NPWML.SC...AK..EI..D.EQ.PE..AH...E.E....PVAEE...L
Retrocopy EEGIVSVSHGMDDLQMNADGVNPWMLSSCNSNAKRGEIKTDPEQMPEFVAHVSSESEGDERPVAEE-LVL

Parental  KELEKRRSLRKRSELNQAAEPLGNQETKDSTSQEVLSELRALSKKLSKENHLSKK
          KE....RS...R...N..A.....QET.DS.SQEVL..L...S.........S..
Retrocopy KE----RSFQERVDPNN-AKLMDGQETEDSDSQEVLQKLNKESHQSDNQKVSSEE

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	6.35 RPM	11.92 RPM
SRP007412_cerebellum	4.39 RPM	13.42 RPM
SRP007412_heart	0.81 RPM	10.27 RPM
SRP007412_kidney	1.69 RPM	9.32 RPM
SRP007412_liver	4.72 RPM	8.77 RPM
SRP007412_testis	13.49 RPM	4.85 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_261 was not detected

EST

19 EST(s) were mapped to retro_mmus_261 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG242485	78665182	78665899	99.1	704	3	692
CA548273	78665621	78666206	100	585	0	585
CA551361	78665621	78666208	100	586	0	585
CA552569	78665621	78666063	100	442	0	442
CA552850	78665621	78666156	99.9	534	1	533
CA553537	78665621	78666188	100	567	0	567
CB520027	78665980	78666281	100	301	0	301
CF153919	78665621	78666120	99.8	498	1	497
CF157317	78665621	78666129	99.9	507	1	506
CF157786	78665621	78666077	100	456	0	456
CF158074	78665621	78666119	99.8	497	1	496
CF158229	78665621	78666123	100	502	0	502
CF158765	78665621	78666079	99.8	457	1	456
CF159941	78665621	78666066	99.8	444	1	443
CF161450	78665621	78666118	100	497	0	497
CF174413	78664357	78665009	99.9	651	1	650
CK335997	78664559	78664876	99.7	316	1	315
DT909247	78665611	78666217	97.9	603	3	595
DT909409	78665611	78666228	99.4	616	1	614

TSS

No TSS is located nearby retro_mmus_261 retrocopy 5' end.

Lab

retro_mmus_261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_261 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261 ,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,