RetrogeneDB ID: retro_mmus_102

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 18:39773683..39775570(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000051732
• Aliases: Pabpc2, Pabp, Pabp+, Pabp2
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pabpc1
• Ensembl ID: ENSMUSG00000022283
• Aliases: Pabpc1, PABP, Pabp1, PabpI, Pabpl1, ePAB
• Description: poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]

Sequence

>retro_mmus_102
ATGAACTCCAGCGACCCAGGCTGTCCCATGGCCTCGCTCTATGTGGGGGACCTGCACCCTGATGTGACTGAGGCGATGCT
CTATGAGAAGTTCAGCTCTGCCGGGCCCATCCTTTCCATCCGGGTATACAGGGACGTGATCACACGCCGTTCCCTGGGCT
ATGCTTCCGTGAACTTTGAGCAGCCTGCTGATGCAGAGCGAGCTTTGGACACCATGAATTTTGATGTCATCAAGGGCAAG
CCGGTCCGCATCATGTGGTCTCAGCGTGATCCATCACTTCGCAGGAGTGGAGTAGGCAATGTGTTCATTAAAAATTTGAA
CAAGACCATTGATAATAAAGCACTGTATGATACATTCTCTGCTTTTGGCAATATCCTTTCCTGCAAGGTGGTTAGCGATG
AGAATGGCTCCAAGGGCCACGGATTTGTACATTTTGAGACAGAGGAGGCAGCAGAAAGAGCCATCGAGAAAATGAACGGG
ATGCTTCTGAATGACCGCAAAGTGTTTGTTGGACGGTTTAAGTCTCAGAAAGAACGAGAAGCCGAGCTTGGAACGGGGAC
CAAGGAGTTTACCAACGTTTACATCAAGAACTTTGGGGACCGCATGGATGACGAGACCCTGAATGGCCTCTTTGGCAGGT
TTGGACAGATCTTAAGTGTGAAAGTCATGACCGATGAAGGTGGGAAATCGAAAGGATTCGGGTTCGTCAGCTTTGAAAGG
CATGAAGATGCGCAGAAAGCGGTGGACGAGATGAATGGTAAAGAACTCAATGGAAAACACATTTATGTTGGTCGAGCGCA
GAAAAAAGATGACCGTCACACAGAACTTAAACACAAATTTGAACAGGTGACACAAGATAAGAGCATCAGATATCAGGGCA
TTAACCTTTATGTGAAAAATCTTGATGATGGCATTGATGATGAACGGCTCCAGAAAGAATTTTCTCCATTTGGAACAATC
ACCAGTACAAAGGTTATGACAGAGGGTGGTCGCAGTAAAGGATTCGGTTTTGTGTGTTTCTCCTCCCCGGAAGAAGCCAC
AAAAGCTGTTTCAGAAATGAATGGGAGAATTGTGGCCACGAAACCACTTTATGTAGCTTTAGCCCAGCGCAAAGAAGAAC
GTCAGGCTCACCTCACTAACCAATATATTCAAAGAATGGCAAGTGTACGATCTGGGCCGAACCCTGTTAACCCCTACCAA
CCAGCATCTTCCAGTTACTCTGTGGCCGCTGTCCCACAGACTCAGAACTGCGTTCCATGCTGCCCTAGCCAAATTGCTCA
ACCAAGGCCAAGTGCTCGCTGGATTGCTCAGGGTTCCCGGCCTCATCCATTCCCCAATGTGCCTGGTGCTATCCACCCAG
CTGCTCCTAGATCGTCGTTGACTACTGTAAGACCAAGCTCTTCACACGTTCAAGTCACGACAGCACATCGCATTACTAAC
ACATCAGCACAGATAACAGGTCAGCGTCCTGCCCCAGCCTCTTCAGCTACAGCGACTCCTGTTCACTCGATTCCACAGTA
CAAGTATGCTGCAGGAGTCCAGAACTCCCAGCAACATCTTAATGCCCAGCTGGCGCAACAGCCCGCTGTTTGCATACAGG
GTCAGGAACCTTGGACTGCTTCCATGTTAGTAACCGCTCCTCAAGAGCCGAAGCAAATGCTGGGTGAAAGGCTATTCCCT
CTCATCCAAGCCATGCACCCGACTCTGGCTGGTAAGATCACGGGCATGTTGCTGGACATTGATAACTCGGAACCACTTCG
TATGCTTGAATCTCCAGTGTCTCGGTGTTCTAGGGCTGAGGAAGCCGTGGCCACACTCCAAGCCCACCAAGTTAAAGAGG
CTGCCCAGAAAGCTGTTGGCAGTACCTCTGGTGTCCCAACTGTTTAA

Alignment

ORF - retro_mmus_102 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.35 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
          MN.S.P..PMASLYVGDLHPDVTEAMLYEKFS.AGPILSIRV.RD.ITRRSLGYA.VNF.QPADAERALD
Retrocopy MNSSDPGCPMASLYVGDLHPDVTEAMLYEKFSSAGPILSIRVYRDVITRRSLGYASVNFEQPADAERALD

Parental  TMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
          TMNFDVIKGKPVRIMWSQRDPSLR.SGVGN.FIKNL.K.IDNKALYDTFSAFGNILSCKVV.DENGSKG.
Retrocopy TMNFDVIKGKPVRIMWSQRDPSLRRSGVGNVFIKNLNKTIDNKALYDTFSAFGNILSCKVVSDENGSKGH

Parental  GFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKEL
          GFVHFET.EAAERAIEKMNGMLLNDRKVFVGRFKS.KEREAELG...KEFTNVYIKNFG..MDDE.L..L
Retrocopy GFVHFETEEAAERAIEKMNGMLLNDRKVFVGRFKSQKEREAELGTGTKEFTNVYIKNFGDRMDDETLNGL

Parental  FGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF
          FG.FG..LSVKVMTDE.GKSKGFGFVSFERHEDAQKAVDEMNGKELNGK.IYVGRAQKK..R.TELK.KF
Retrocopy FGRFGQILSVKVMTDEGGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKHIYVGRAQKKDDRHTELKHKF

Parental  EQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
          EQ..QD...RYQG.NLYVKNLDDGIDDERL.KEFSPFGTITS.KVM.EGGRSKGFGFVCFSSPEEATKAV
Retrocopy EQVTQDKSIRYQGINLYVKNLDDGIDDERLQKEFSPFGTITSTKVMTEGGRSKGFGFVCFSSPEEATKAV

Parental  TEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA
          .EMNGRIVATKPLYVALAQRKEERQAHLTNQY.QRMASVR..PNPV.NPYQPA..S.Y..AA.PQTQN..
Retrocopy SEMNGRIVATKPLYVALAQRKEERQAHLTNQYIQRMASVRSGPNPV-NPYQPA-SSSYSVAAVPQTQNCV

Parental  AYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTM
          ...P.SQIAQ.RPS.RW.AQG.RPHPF.N.PGAI.PAAPR....T.RP.SS.V..V....R..NTS.Q..
Retrocopy PCCP-SQIAQPRPSARWIAQGSRPHPFPNVPGAIHPAAPRSSLTTVRPSSSHV-QVTTAHRITNTSAQIT

Parental  GPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQ
          G.RPA.A..A....V...PQYKYAAGV.N.QQHLNAQ.....QQPAV..QGQEP.TASML..A.PQE.KQ
Retrocopy GQRPAPASSATATPVHSIPQYKYAAGVQNSQQHLNAQ---LAQQPAVCIQGQEPWTASMLVTA-PQEPKQ

Parental  MLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSA
          MLGERLFPLIQAMHP.LAGKITGMLL.IDNSE.L.MLESP.S..S...EAVA.LQAHQ.KEAAQKAV.S.
Retrocopy MLGERLFPLIQAMHPTLAGKITGMLLDIDNSEPLRMLESPVSRCSRAEEAVATLQAHQVKEAAQKAVGST

Parental  TGVPTV
          .GVPTV
Retrocopy SGVPTV

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	0.02 RPM	112.73 RPM
SRP007412_cerebellum	0.00 RPM	87.88 RPM
SRP007412_heart	0.03 RPM	95.29 RPM
SRP007412_kidney	0.02 RPM	201.93 RPM
SRP007412_liver	0.14 RPM	223.25 RPM
SRP007412_testis	683.25 RPM	1753.45 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_102 was not detected

EST

6 EST(s) were mapped to retro_mmus_102 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI037666	39774282	39774787	99.8	492	0	483
AI385989	39773684	39774197	98.7	505	7	498
BB614478	39773585	39774218	97.3	613	4	597
CB274492	39773599	39774189	99.4	586	4	582
CB274730	39774394	39774968	100	574	0	574
CF104603	39773669	39774241	99.9	571	1	570

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_59278	1058 libraries	7 libraries	1 library	0 libraries	6 libraries
TSS #2	TSS_59279	1061 libraries	5 libraries	2 libraries	0 libraries	4 libraries
TSS #3	TSS_59280	1064 libraries	4 libraries	1 library	1 library	2 libraries

The graphical summary, for retro_mmus_102 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_102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_102 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_265

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 55 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000348	1 retrocopy	retro_amel_1650,
Choloepus hoffmanni	ENSCHOG00000008178	1 retrocopy	retro_chof_2531,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000012917	1 retrocopy	retro_cpor_1324,
Dasypus novemcinctus	ENSDNOG00000008718	2 retrocopies	retro_dnov_1530, retro_dnov_2259,
Felis catus	ENSFCAG00000001874	1 retrocopy	retro_fcat_1927,
Homo sapiens	ENSG00000070756	1 retrocopy	retro_hsap_88,
Gorilla gorilla	ENSGGOG00000006785	1 retrocopy	retro_ggor_1986,
Myotis lucifugus	ENSMLUG00000012245	1 retrocopy	retro_mluc_579,
Macaca mulatta	ENSMMUG00000017786	2 retrocopies	retro_mmul_1462, retro_mmul_895,
Monodelphis domestica	ENSMODG00000006222	4 retrocopies	retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Mus musculus	ENSMUSG00000022283	2 retrocopies	retro_mmus_102 , retro_mmus_2164,
Mus musculus	ENSMUSG00000040043	1 retrocopy	retro_mmus_1530,
Nomascus leucogenys	ENSNLEG00000003142	3 retrocopies	retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus	ENSOCUG00000004354	1 retrocopy	retro_ocun_13,
Pongo abelii	ENSPPYG00000018790	3 retrocopies	retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus	ENSPVAG00000016640	2 retrocopies	retro_pvam_10, retro_pvam_855,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii	ENSSHAG00000011267	1 retrocopy	retro_shar_24,
Sus scrofa	ENSSSCG00000006063	2 retrocopies	retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus	ENSSTOG00000016395	2 retrocopies	retro_itri_139, retro_itri_48,
Tarsius syrichta	ENSTSYG00000004229	2 retrocopies	retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus	ENSTTRG00000004689	2 retrocopies	retro_ttru_1050, retro_ttru_1812,
Vicugna pacos	ENSVPAG00000003865	4 retrocopies	retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,