RetrogeneDB ID: retro_rnor_1625

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:93558574..93559541(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RGD1307947
• Ensembl ID: ENSRNOG00000006973
• Aliases: None
• Description: None

Sequence

>retro_rnor_1625
CTTGGAGCAGTGGAAGATGCTGTGTGTGCATGTTTGTGACAGACGTGAAAGCTGACCCTTCATCTAAGTGGGAGCATCAG
AAATTTAAAGTTTTGTTAACTGAAATTCCAAGTGAAAAGGCGTTAGATGTAGATGTGTACCATGCGGTTGCAATAGAAAA
AGTGAATGGAACATGTTTGTTTCTATGTTACTTAACTACAATGGTCAGCTACACCTTTGGGCGCGACTAGGCAGAAAACC
TAACGAGCAAGTTGACAAAAGCTTTAAAAAATTTCTACATTCAAAGAAAATGCAAGAGTTTCATTGCAAAACTGAGGAAG
ACTTCAAGCCTGTCCCAGAGTGCTGGGTACCAGCAAAGGAAATAGAAAAACAGAACAAGAAGTCAGTACCAGACAAAAAC
GGAACCATTCCTGGTTGGGTACCAGTAGGAAAGAACAGCAAGCAACATTGCTGGCACTCGTCTGTAGTGAGTTATGAGTT
TGAAATTGCTCTGGTACTAAGGCACCATCCTGAGGATCTTGGGGTTTTGAAAATTAGTGCTGTTCTCTTGTCAGAGCTTT
TAGAGCAAACTCTGGAGCTGATAAGAACGAATATCAATGGAAACCCGTATGGGTTAGGAAGCAAGAAATACCCATTACAT
TTTCTTACACCACATGGAGCATTCCAGGTCAGAAATCTGCCTACACTGAAACACAATGACCTGCTGTCCTGGTTTGGAGA
CTGCAGAGAGAGTCAAATAGAAGGGATTGTGTAGCATTGCGGTAATGGATGTTTAATTAAGGTTCACCGTTACCATCTTG
GTTTATGTTGGCCACTTCTGGATACCTACATTAAGATCAAACCAGTTATTATTAACATGAACCTGGACAAATATGAATGT
TCTTTTGATCACCAGTCTTCGTTTAATTAGTTTTCAAAAATAGATAAACAGAAATTTGATAGGCTCAAAGATATAACCCT
TGATGTA

Alignment

ORF - retro_rnor_1625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.67 %
• Parental protein coverage: 99.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LGSVQ-RKMPCVFVTEVKAEPSAKREHQPFKVLATETLSEKALDADVYNAVATEKVDGTC-C-YVT-NYK
          LG.V..R...C.FVT.VKA.PS.K.EHQ.FKVL.TE..SEKALD.DVY.AVA.EKV.GTC.C.YVT.NY.
Retrocopy LGAVE<RCCVCMFVTDVKADPSSKWEHQKFKVLLTEIPSEKALDVDVYHAVAIEKVNGTC>CFYVT>NYN

Parental  GQPYLWARLDRKPNKQADKRFKKFLHSKENAKEFHWNTEEDFKPVPECWIPAKEIEKQNGKPVPDENGHI
          GQ..LWARL.RKPN.Q.DK.FKKFLHSK....EFH..TEEDFKPVPECW.PAKEIEKQN.K.VPD.NG.I
Retrocopy GQLHLWARLGRKPNEQVDKSFKKFLHSKK-MQEFHCKTEEDFKPVPECWVPAKEIEKQNKKSVPDKNGTI

Parental  PGWVPVEKNSKQYCWHSSVVSYEFGIALVLRHHPDDPGVLEISAVPLSELLEQTLELIGTNINGNPYGLG
          PGWVPV.KNSKQ.CWHSSVVSYEF.IALVLRHHP.D.GVL.ISAV.LSELLEQTLELI.TNINGNPYGLG
Retrocopy PGWVPVGKNSKQHCWHSSVVSYEFEIALVLRHHPEDLGVLKISAVLLSELLEQTLELIRTNINGNPYGLG

Parental  SKKYPLHFLTPHGAFQVRNLPTLKHNDLLSWFEGCREGQIEGIVWHCGDGCLIKVHRHHLGLCWPLPDTY
          SKKYPLHFLTPHGAFQVRNLPTLKHNDLLSWF..CRE.QIEGIV.HCG.GCLIKVHR.HLGLCWPL.DTY
Retrocopy SKKYPLHFLTPHGAFQVRNLPTLKHNDLLSWFGDCRESQIEGIV*HCGNGCLIKVHRYHLGLCWPLLDTY

Parental  MNSKPVIINMNLDKYDCAFDHQSLFNKFSKIDKQKFDRLKDITLDI
          ...KPVIINMNLDKY.C.FDHQS.FN.FSKIDKQKFDRLKDITLD.
Retrocopy IKIKPVIINMNLDKYECSFDHQSSFN*FSKIDKQKFDRLKDITLDV

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	13.95 RPM
SRP017611_kidney	0.00 RPM	7.12 RPM
SRP017611_liver	0.00 RPM	2.82 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1625 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1625 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1625 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000011011	1 retrocopy	retro_chof_1262,
Homo sapiens	ENSG00000133641	1 retrocopy	retro_hsap_3984,
Gorilla gorilla	ENSGGOG00000005986	1 retrocopy	retro_ggor_2674,
Loxodonta africana	ENSLAFG00000013286	1 retrocopy	retro_lafr_706,
Macaca mulatta	ENSMMUG00000015860	1 retrocopy	retro_mmul_715,
Nomascus leucogenys	ENSNLEG00000005396	1 retrocopy	retro_nleu_1905,
Pan troglodytes	ENSPTRG00000005277	1 retrocopy	retro_ptro_2704,
Rattus norvegicus	ENSRNOG00000006973	1 retrocopy	retro_rnor_1625 ,
Tupaia belangeri	ENSTBEG00000005256	1 retrocopy	retro_tbel_94,
Tarsius syrichta	ENSTSYG00000014665	1 retrocopy	retro_tsyr_1572,