RetrogeneDB ID: retro_rnor_1365

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 18:75230921..75231534(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hnrpdl
• Ensembl ID: ENSRNOG00000002270
• Aliases: Hnrnpdl, Hnrpdl, hnRNP DL
• Description: Heterogeneous nuclear ribonucleoprotein D-like [Source:UniProtKB/Swiss-Prot;Acc:Q3SWU3]

Sequence

>retro_rnor_1365
AAAATGTTTATTGGCGACTTGAGCTGGGACATAAAGTGATAAAGATGTGACTGAGTGCTTGTCTTGATTTGGGAAAGTTA
TAGATTGCACAATTAAAGCAGATCTAGCCATTGGGAGATTGAGAGGGTGTGCATTTGAGCCTTTCAAAGACACTGCTACT
GATAATAGATGCTGGAAACGAACGAATGGAAGCTGTGTCATAAGTGGACACATCCCGAATCCTTGAGACATTAAAAAGGA
AGGAACCCCTTAAAAAGATTTTGTGGGTGGATTGAATTCAGATAGTTCCAAAAGCAAATTTAAGGTTATTTTAGAGCCTT
GGAAAGTGAAAACATAGAACTTCCAGCGGGTACAAAAACAAATGAAAGAAGAGGATTCACTCTATAACTGACCCGGATGA
AGAGTAAGGAAAGAAATCGTTAGGAAGCAAAGAATATCAAATAGTTTCTGGGAAGCAAAGGTCAGAGTTGCACAACCCAA
GGTATTTACAGGCAGCAATACCAAGAGCAGAAAGGAGGAAGAAATGCTACTCCTGCTCGAAGGTCACTCTAGGGGACAGA
GATGAGGTGAGGGCCAAAACTGAACCCAAGGATTTAATAACTGCTGGGATCAA

Alignment

ORF - retro_rnor_1365 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.92 %
• Parental protein coverage: 64.6 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  KMFIGGLSWDT-SKKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDK-VLELKEHKLDGK
          KMFIG.LSWD..S.KD.TE.LS.FG.V.DCTIK.D...GR.RG..F..FKD.A......LE..E.KL..K
Retrocopy KMFIGDLSWDI>SDKDVTECLS*FGKVIDCTIKADLAIGRLRGCAFEPFKDTATDNR<MLETNEWKLCHK

Parental  LIDPKRAK-ALKGKEPPKKV-FVGGLSPDTS-EEQIKEYFGAFGEIENIELPMDTKTNERRGFCF-ITYT
          ...P......LK.KEP.KK..FVGGL..D.S...QI..YF.A..E.ENIELP..TKTNERRGF...IT..
Retrocopy WTHPESLR<TLKRKEPLKKI<FVGGLNSDSS<QKQI*GYFRAL-ESENIELPAGTKTNERRGFTL<ITDP

Parental  DEEPVKKLLESRYHQIGSGK-CEIKVAQPKE-VYRQQQQQQKGGRGAAAGGR-GGARGRGRGQGQNWNQG
          DEE..KK.L.S...QI.SGK.....VAQPK...YRQQ.Q....G...A...R.G..RG...G.GQN..QG
Retrocopy DEE*GKKSLGSKEYQIVSGK<AKVRVAQPKV<IYRQQYQ-EQKGGRNATPAR>GHSRGQR*GEGQN*TQG

Parental  FNNYYDQ
          FNN..DQ
Retrocopy FNNCWDQ

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	109.64 RPM
SRP017611_kidney	0.00 RPM	43.33 RPM
SRP017611_liver	0.00 RPM	32.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1365 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1365 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1365 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014804	2 retrocopies	retro_btau_1827, retro_btau_461,
Canis familiaris	ENSCAFG00000008940	1 retrocopy	retro_cfam_1086,
Choloepus hoffmanni	ENSCHOG00000000160	8 retrocopies	retro_chof_115, retro_chof_1470, retro_chof_2108, retro_chof_2370, retro_chof_533, retro_chof_59, retro_chof_741, retro_chof_890,
Choloepus hoffmanni	ENSCHOG00000003275	2 retrocopies	retro_chof_1578, retro_chof_18,
Cavia porcellus	ENSCPOG00000015619	5 retrocopies	retro_cpor_1110, retro_cpor_1318, retro_cpor_264, retro_cpor_274, retro_cpor_567,
Dipodomys ordii	ENSDORG00000000968	1 retrocopy	retro_dord_145,
Equus caballus	ENSECAG00000022692	1 retrocopy	retro_ecab_1082,
Loxodonta africana	ENSLAFG00000008612	1 retrocopy	retro_lafr_650,
Microcebus murinus	ENSMICG00000001445	4 retrocopies	retro_mmur_1016, retro_mmur_1570, retro_mmur_1572, retro_mmur_557,
Myotis lucifugus	ENSMLUG00000014452	2 retrocopies	retro_mluc_1140, retro_mluc_1761,
Mustela putorius furo	ENSMPUG00000014753	2 retrocopies	retro_mputfur_1359, retro_mputfur_600,
Nomascus leucogenys	ENSNLEG00000008636	1 retrocopy	retro_nleu_673,
Oryctolagus cuniculus	ENSOCUG00000013805	1 retrocopy	retro_ocun_505,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
Ochotona princeps	ENSOPRG00000007178	3 retrocopies	retro_opri_1075, retro_opri_623, retro_opri_703,
Procavia capensis	ENSPCAG00000011543	1 retrocopy	retro_pcap_366,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Rattus norvegicus	ENSRNOG00000002270	1 retrocopy	retro_rnor_1365 ,
Rattus norvegicus	ENSRNOG00000011175	3 retrocopies	retro_rnor_1824, retro_rnor_2043, retro_rnor_2339,
Rattus norvegicus	ENSRNOG00000036839	17 retrocopies	retro_rnor_1001, retro_rnor_1322, retro_rnor_1658, retro_rnor_1770, retro_rnor_1786, retro_rnor_1846, retro_rnor_1987, retro_rnor_2194, retro_rnor_2482, retro_rnor_2551, retro_rnor_2619, retro_rnor_2657, retro_rnor_2881, retro_rnor_2944, retro_rnor_2945, retro_rnor_2965, retro_rnor_2969,
Sorex araneus	ENSSARG00000009961	1 retrocopy	retro_sara_421,