RetrogeneDB ID: retro_rnor_560

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:3559024..3559590(-)
• Located in intron of: ENSRNOG00000014996

Retrocopy information

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

Parental gene information

• Parental gene symbol: Hn1l
• Ensembl ID: ENSRNOG00000024661
• Aliases: Hn1l, RGD1305117
• Description: Hematological and neurological expressed 1-like protein [Source:UniProtKB/Swiss-Prot;Acc:Q5BK20]

Sequence

>retro_rnor_560
ATGTTCCGGGGCACGGACAGCCAAGCTAGCAAGTCGGGCATCAGATCCATGAAACCCCTGGGGGGAGAGTCAAACGATAT
TTTTGGAAGTCCAGAAGAAGGTGTTCCTTCAAGCGAGCCTCGTAGGATGGCATCTAGTATTTTTGGACCAACTGAAGAAC
CTAAAAACATACCCAAGAGGACAAATCCTCCAGGAGGCAAAGGAAGTGGAATCTTTGATGAACCAACTCCTGTGCAAACT
GGACAACGTCTGAACCCACCCGGTGGAAAGACCAGTGACACATGTGGGTCCCCAGTCACTGCCACTGCACCTCTGGCACA
CCCTAACAAGCCCACGGATCATGTCTTGCTGTGTGCAGGGGAAGACTGAAAGTCTGACCTGAAAGCTGCCACAAACTCCA
CAGCCAGAGGAGAGCAGGGCGAGAAAGGAAGCTCAGCAGAAGCAGAGCCTGCAAAGATACCGGAGCCCACTCCTACAGTT
GACAGCCATGACCCAGACTGGGGCCTCGACCTCGCTCCCACAACCAAGTCCTGAACCCAGCAGGAGGCAAATCCAGCATC
TCCTTC

Alignment

ORF - retro_rnor_560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.95 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFRGADGQASKSGFRSMKPPGGESNDIFGSPEEGVPSSKPHRMASNIFGPTEEPKNIPKRTNPPGGKGSG
          MFRG.D.QASKSG.RSMKP.GGESNDIFGSPEEGVPSS.P.RMAS.IFGPTEEPKNIPKRTNPPGGKGSG
Retrocopy MFRGTDSQASKSGIRSMKPLGGESNDIFGSPEEGVPSSEPRRMASSIFGPTEEPKNIPKRTNPPGGKGSG

Parental  IFDESTPVQTRQRLNPPGGKTSDIFGSPVTATAPLAHPNKPKDHVLLCEGEDCKSDLKAATNSTPRGEQG
          IFDE.TPVQT.QRLNPPGGKTSD..GSPVTATAPLAHPNKP.DHVLLC.GED.KSDLKAATNST.RGEQG
Retrocopy IFDEPTPVQTGQRLNPPGGKTSDTCGSPVTATAPLAHPNKPTDHVLLCAGED*KSDLKAATNSTARGEQG

Parental  EKGSSTEAEPAKIPEPIPTVDSHE-PRLGPRPRSHNKVLNPPGGKSSISF
          EKGSS.EAEPAKIPEP.PTVDSH..PRLGPRPRSHN.VLNP.GGKSSISF
Retrocopy EKGSSAEAEPAKIPEPTPTVDSHD<PRLGPRPRSHNQVLNPAGGKSSISF

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	0.29 RPM	9.99 RPM
SRP017611_kidney	0.42 RPM	32.52 RPM
SRP017611_liver	0.00 RPM	33.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_560 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008232	1 retrocopy	retro_amel_1019,
Cavia porcellus	ENSCPOG00000005352	2 retrocopies	retro_cpor_749, retro_cpor_892,
Dipodomys ordii	ENSDORG00000007521	1 retrocopy	retro_dord_269,
Macropus eugenii	ENSMEUG00000008873	4 retrocopies	retro_meug_1471, retro_meug_1628, retro_meug_189, retro_meug_258,
Mus musculus	ENSMUSG00000024165	3 retrocopies	retro_mmus_1204, retro_mmus_655, retro_mmus_709,
Oryctolagus cuniculus	ENSOCUG00000015551	1 retrocopy	retro_ocun_275,
Pteropus vampyrus	ENSPVAG00000016673	1 retrocopy	retro_pvam_99,
Rattus norvegicus	ENSRNOG00000024661	2 retrocopies	retro_rnor_25, retro_rnor_560 ,
Sorex araneus	ENSSARG00000012440	1 retrocopy	retro_sara_335,
Sarcophilus harrisii	ENSSHAG00000012700	1 retrocopy	retro_shar_184,
Tursiops truncatus	ENSTTRG00000011377	1 retrocopy	retro_ttru_429,