RetrogeneDB ID: retro_rnor_2321

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:114602388..114603506(+)
• Located in intron of: ENSRNOG00000008082

Retrocopy information

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

Parental gene information

• Parental gene symbol: Pabpc1
• Ensembl ID: ENSRNOG00000008639
• Aliases: Pabpc1, Pabp, Pabp1
• Description: Polyadenylate-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9EPH8]

Sequence

>retro_rnor_2321
TATGTTGGTCGAGCTCAGAAAAAAGTGGAACGGCAGACGGAACTTAAGCGCAAATTTGAGCAGATGAAACAAGACAGGAT
CACCAGATATCAGGGTGTTAACCTTTATGTGAAAAATCTTGATGACGGTATTGATGATGAGCGTCTCCGGAAAGTGTTTT
CTCCATTTGGTACAATCACTAGTGCAAAAGTAATGATGGAGGATGGGCGCAGCAAAGGATTCGGTTTTATATGTTTCTCC
TCCCCTGAAGAAGCCATAAAGCAGTTACGGAGATGAATGGCAGAATTGTGGCCACCAAGCCACTCTATGTAGCTTTAGCT
CAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTATATGAAGAGGATGGCAAGTGTACGAGCTGTGCCCAACCC
TGTGATCAACCCCTACCAGCCAGCACCTCCGTCAGGTTACTTCATGGCAGCTATCCCACAGACTCAGAACGATGCTGCAT
ACTACCCTCCTAGCCGAATTGCTCAACTAAGTCCTCACTGGATTGCTCAGGGTGCCAGACCTCATCCGTTCCAGAATATG
CCCGGTGCTAACCGCCCAGCTGCTCCTAGACCACCATTTAGTACGATGAGACCAGCTTCCTCACAGGTTCCCCGAGTCAT
GCTAACACAGGGTGTTGCTAACACATCAACACAGACAATGGGTCCACGTCCTGCAGCTGCTGCTACTGCAGCTACTCCTG
CTGTCCGCACTGTTCCCCAGTATAAATATGCTGCGGGAGTCTGCAATCCCCAGCAACATCTTAATGCACACCCACAAGTT
ACCATGCAACAGCCTGCGGTTCATGTGCAAGGTCAAGAACCTTTAACTGCTTCCATATTGGCATCTGCACCCCCGCAAGA
GCAAAAGCAAATGTTGGGTGAACGGCTGTTTCCTCTTATTCAAGCCATGCAGCCTTCTCTTACTGGCAAAGTTACTGGCA
TGCTGTTGGAGATTGATAACCCAGAATTACTTCACATGCTTGAGTCTCCAGAGTCTCTCTTCTCAAAGGTCAATGAAGCT
GTAGCTGTACTACAAGCCCGCCAAGCGAAAGAGGCTGCCCAGAAAGCAGTGAGCAGTGCCACTGGTGTCCCAACTGTC

Alignment

ORF - retro_rnor_2321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.09 %
• Parental protein coverage: 58.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGR
          YVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRK.FSPFGTITSAKVMME.GR
Retrocopy YVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKVFSPFGTITSAKVMMEDGR

Parental  SKGFGFVCFSSPEEATK-AVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPY
          SKGFGF.CFSSPEEA.K.AVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYM.RMASVRAVPNPVINPY
Retrocopy SKGFGFICFSSPEEAIK<AVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMKRMASVRAVPNPVINPY

Parental  QPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPAS
          QPAPPSGYFMAAIPQTQN.AAYYPPS.IAQL..SP.W.AQGARPHPFQNMPGA.RPAAPRPPFSTMRPAS
Retrocopy QPAPPSGYFMAAIPQTQNDAAYYPPSRIAQL--SPHWIAQGARPHPFQNMPGANRPAAPRPPFSTMRPAS

Parental  SQVPRVMSTQRVANTSTQTMGPRPAAAATAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQ
          SQVPRVM.TQ.VANTSTQTMGPRPAAAATAATPAVRTVPQYKYAAGV.NPQQHLNA.PQVTMQQPAVHVQ
Retrocopy SQVPRVMLTQGVANTSTQTMGPRPAAAATAATPAVRTVPQYKYAAGVCNPQQHLNAHPQVTMQQPAVHVQ

Parental  GQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLRSKVDEA
          GQEPLTAS.LASAPPQEQKQMLGERLFPLIQAM.PSL.GK.TGMLLEIDN.ELLHMLESPESL.SKV.EA
Retrocopy GQEPLTASILASAPPQEQKQMLGERLFPLIQAMQPSLTGKVTGMLLEIDNPELLHMLESPESLFSKVNEA

Parental  VAVLQAHQAKEAAQKAVNSATGVPTV
          VAVLQA.QAKEAAQKAV.SATGVPTV
Retrocopy VAVLQARQAKEAAQKAVSSATGVPTV

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	141.49 RPM
SRP017611_kidney	0.07 RPM	275.36 RPM
SRP017611_liver	0.07 RPM	207.09 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2321 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2321 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2321 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 25 parental genes, and 50 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	ENSMUSG00000022283	2 retrocopies	retro_mmus_102, retro_mmus_2164,
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	ENSRNOG00000003076	1 retrocopy	retro_rnor_1374,
Rattus norvegicus	ENSRNOG00000008639	3 retrocopies	retro_rnor_1228, retro_rnor_2321 , retro_rnor_265,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
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,