RetrogeneDB ID: retro_rnor_1994

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:168744618..168746278(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000005835
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ptbp1
• Ensembl ID: ENSRNOG00000010448
• Aliases: Ptbp1, Ptb, Pybp, Pybp1, Pybp2
• Description: polypyrimidine tract-binding protein 1 isoform b [Source:RefSeq peptide;Acc:NP_071961]

Sequence

>retro_rnor_1994
ATGGACCGCATCATCCCAGACATAGCAGTCGGTACAAAGTGGGGATCCGATGAGCTCTTTTCCACACATGTCAGCAACGG
CCCCTTCACCATGAGCAGCTTGGCCTCAGTAGCCAATGGAAATGATAGCAAGAAGTTCAAAGGTGACAATAGGAGTACAG
GAGTTCCTTCCAGAGTCATCCATGTCCAAAAGCTACCTAGTAATGTCACTGAGGGGAAGGTCATCTCCCTGGAGCTGCCC
TTTGGGAACGTTACCAACCTCCTTATGCTGAAGGGGAAGAACCAGGCCTCCATTGAAATGAGCACAGAGGAGGCTGCCAA
CACTATGGTTAACTACTACACATGGGTGGCGCCAGTGCTTCATGGACAGCCCATCTACATCCAGTTCTCCAACCACAAGG
AGTTCAAAACCCACAGCTCGCCCAACCAGGCACGTGCCCAGGCAGCCCTGCAGGCTGTGAACTCTGTACAGTCAGGAAAC
CTGGCCTTGGCAGCCTCGGCTGCTGCGGTGGATGCAGGAATGGCAAAGGCAGGCCAGAGGCCAGTTATCAGGTTCATCGT
GGAGAACCTTTTCTACCCAGTGACCCTGGACGCACTGCACCAGATCTTCTCTAAGTTTGGCGCAGTCCTGAAGATCACAC
GTTCACCAAGAACAACCAGTTCCAGGTGCTGCTGCAACATGCTGACCCTGTGAGCGCCCAGCATGCCAAGTTGTCCCTGG
ATGGCCAGAACATCTACAATGCTTGTTGTACGCTACACATCAACTTCTCCAAGCTCACCAGTCTCGACGTAAAATACAAT
AACGACAAGAGCAGAGATTACACTCGACCTGCTCTGCCCTCTGGAGACAGCCAGCCATCACTGGCCAGGCCATGGCAGTA
GTCTTCTTTGTGCCCGGCATAACGTCAGACTCTCCAAATGCAGGAGCCGGGTTCCCTCTCACCTTTGCCACCCCTCAGGC
TGCAGGCCTCTCTGTTCCTAATGTCCATGGAGCCCTGGCCACCCTGGCCATACCCTCTGCTGCGGTTGCTGCAGCCGGCC
GCATTGCCATCCCAGGGTTGGCAGGAGTTGGGAATTCCATCCTTTTGGTCAGCAACCTGAACCCTGAGAGAGTCACAGCC
CAAAGCCTCTTTATTCTCTTCAGCATCTACGGTGATGTGAAGCGGATGAAGATCCTGTTCAATAAGAAGGAGAATGCACT
CCTGCAGATGGCAGACGGCAACCAGGCCCAGCTGGCCATGAGCCACCTGAACGGGCACAAGCTGGATGGGAAGTCAGTAC
GCATCACACCGTCAAAGCATCAGAGCGTGCAGCTGCCTCATGAGAGACAGGAGGACCAGGGACTGACCAAGAATTATGAC
AGCTCACCACTGCATTGCGTCCAGAAACCAGGCTCCAAGAACTTCCAGAACATCTTTCCACCCTCAGCTACCCTGCACCT
CTCCAACATCCCGCCCTCTGTGTCAGAGGATGGCCTCAAGAGCCTCTTCTCCAGCAATGGTGATATGGCAAAAGGCTTCA
AGTTCTTCAAGAAGGACCACAAGATGGCACTGATCCAGATGGGCTCTGTGGAGGAGGCAGTGCAGGCACTAATTGAGCTG
CACAGCCATGACCTGGGGGAGAACTACCACCCGAGAGTGTTCTTTTCCAAGTCCACCATC

Alignment

ORF - retro_rnor_1994 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.13 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDGIVPDIAVGTKRGSDELFSTCVSNGPFIMSSSASAANGNDSKKFKGDNRSTGVPSRVIHVRKLPSDVT
          MD.I.PDIAVGTK.GSDELFST.VSNGPF.MSS.AS.ANGNDSKKFKGDNRSTGVPSRVIHV.KLPS.VT
Retrocopy MDRIIPDIAVGTKWGSDELFSTHVSNGPFTMSSLASVANGNDSKKFKGDNRSTGVPSRVIHVQKLPSNVT

Parental  EGEVISLGLPFGKVTNLLMLKGKNQAFIEMSTEEAANTMVNYYTSVAPVLRGQPIYIQFSNHKELKTDSS
          EG.VISL.LPFG.VTNLLMLKGKNQA.IEMSTEEAANTMVNYYT.VAPVL.GQPIYIQFSNHKE.KT.SS
Retrocopy EGKVISLELPFGNVTNLLMLKGKNQASIEMSTEEAANTMVNYYTWVAPVLHGQPIYIQFSNHKEFKTHSS

Parental  PNQARAQAALQAVNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVL
          PNQARAQAALQAVNSVQSGNLALAASAAAVDAGMA.AGQ.PV.R.IVENLFYPVTLD.LHQIFSKFG.VL
Retrocopy PNQARAQAALQAVNSVQSGNLALAASAAAVDAGMAKAGQRPVIRFIVENLFYPVTLDALHQIFSKFGAVL

Parental  KII-TFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDL
          KI..TFTKNNQFQ.LLQ.ADPVSAQHAKLSLDGQNIYNACCTL.I.FSKLTSL.VKYNNDKSRDYTRP.L
Retrocopy KIT<TFTKNNQFQVLLQHADPVSAQHAKLSLDGQNIYNACCTLHINFSKLTSLDVKYNNDKSRDYTRPAL

Parental  PSGDSQPSL-DQTMAAAFGAPGIMSASPYAGV--PSHLCHPSVAGLSVPNVHGALAPLAIPSAAAAAAAA
          PSGDSQPSL..Q.MA..F..PGI.S.SP.AG...P.....P..AGLSVPNVHGALA.LAIPS..AA.AAA
Retrocopy PSGDSQPSL<GQAMAVVFFVPGITSDSPNAGAGFPLTFATPQAAGLSVPNVHGALATLAIPS--AAVAAA

Parental  GRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKENALVQMADGSQAQLAMSH
          GRIAIPGLAG.GNS.LLVSNLNPERVT.QSLFILF..YGDV.R.KILFNKKENAL.QMADG.QAQLAMSH
Retrocopy GRIAIPGLAGVGNSILLVSNLNPERVTAQSLFILFSIYGDVKRMKILFNKKENALLQMADGNQAQLAMSH

Parental  LNGHKLHGKSVRITLSKHQSVQLPREGQEDQGLTKDYGSSPLHRFKKPGSKNFQNIFPPSATLHLSNIPP
          LNGHKL.GKSVRIT.SKHQSVQLP.E.QEDQGLTK.Y.SSPLH...KPGSKNFQNIFPPSATLHLSNIPP
Retrocopy LNGHKLDGKSVRITPSKHQSVQLPHERQEDQGLTKNYDSSPLHCVQKPGSKNFQNIFPPSATLHLSNIPP

Parental  SVSEDDLKSLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIELHNHDLGENHHLRVSFSKSTI
          SVSED.LKSLFSSNG...KGFKFF.KD.KMALIQMGSVEEAVQALIELH.HDLGEN.H.RV.FSKSTI
Retrocopy SVSEDGLKSLFSSNGDMAKGFKFFKKDHKMALIQMGSVEEAVQALIELHSHDLGENYHPRVFFSKSTI

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
SRP017611_brain	0.00 RPM	33.36 RPM
SRP017611_kidney	0.00 RPM	189.04 RPM
SRP017611_liver	0.07 RPM	66.90 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1994 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1994 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1994 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Dasypus novemcinctus	ENSDNOG00000000882	1 retrocopy	retro_dnov_982,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Mus musculus	ENSMUSG00000006498	1 retrocopy	retro_mmus_1072,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994 , retro_rnor_2478,