RetrogeneDB ID: retro_rnor_614

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:163634935..163635807(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam98a
• Ensembl ID: ENSRNOG00000030328
• Aliases: Fam98a, RGD1305486
• Description: Protein FAM98A [Source:UniProtKB/Swiss-Prot;Acc:Q5FWT1]

Sequence

>retro_rnor_614
CGTTTGGATGTCATTGTCCAGTCCTCTGGCTGGTCTGACCTAGCTAAGAGTCAGACAGAAAAATTAGCTAAAGTTTAGCA
GCCCAAGCGTTCTGTCTTGTCTCCTAAAGGTACTATTTCCGTTGCTCATCTTTTGGCCACCAGACAAGACTTGTCAAAGA
TTTTAAGGACAAGTAATGGGTCCATAGGAGAAAAGACTGCCTGTGCCATTAATAAGGTGTTGATGGGCAGGGTGTCTGAC
AGAGGTGGCAGACCTAGTGAAATTGAACCCCTGCTTCCAAAGATGCCACCGTGGCAGAAAAGACAAGATGGCCCCCAGCA
GCAAGCAGGAGGCTGAGGTGGAGGGAGATTTGGTTATAAACATTCCTCATATGGAGGACGAGGAGGTCATGAACAAGGAG
GGTGAGGTGGATGTGGTGGCTATGACCATGGTGGGTGAGGGGGAGGAAGAGGAAAAAAGCATCAAGGAGGCTGGCCAGAT
GGAGGGAGTGGAGGTGGAGGTGGCTACCAGGATGGCGGTTATCGAGATCCGGGCTTCCAGCCTGGTGGCTATCATGGTGG
CCACAGCAGTGGCTATCAAGGGGGTGGAGATGGTGGTTTCCAAACATCTTCATATAGAGGAAGTGGATACCAGGGCAGTG
GATACCAGCAGGACAATAGATACCAAGATGGTGGGCACCATGGCGAATAAGGCAGTGGTCTTGGGGGAAGAGGTGGTTGA
GGAGGTCTGGAAGGATGGGGAAGCCAGGGATGAGGCTGGGGAGGAAGAAGAATCCAGACTTAACACTAGGGGGCCAGTTT
GAACAGCATTTCCAACATGGAGGCTATCAGTATAGTCATTCTGGATTTGGACAAGGAAGACATCATACTAGT

Alignment

ORF - retro_rnor_614 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.3 %
• Parental protein coverage: 56.5 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLDVTVQSFGWSDRAKSQTEKLAKVYQPKRSVLSPKGNISIAHLLAARQDLSKILRTSSGSIREKTACAI
          RLDV.VQS.GWSD.AKSQTEKLAKV.QPKRSVLSPKG.IS.AHLLA.RQDLSKILRTS.GSI.EKTACAI
Retrocopy RLDVIVQSSGWSDLAKSQTEKLAKV*QPKRSVLSPKGTISVAHLLATRQDLSKILRTSNGSIGEKTACAI

Parental  NKVLMGRVPDRGGRPNEIEPPPPEMPPWQKRQDGPQQQAGGRGGGRGGYEHSSYGGRGGHEQGGRGGRGG
          NKVLMGRV.DRGGRP.EIEP..P.MPPWQKRQDGPQQQAGG.GGGR.GY.HSSYGGRGGHEQGG.GG.GG
Retrocopy NKVLMGRVSDRGGRPSEIEPLLPKMPPWQKRQDGPQQQAGG*GGGRFGYKHSSYGGRGGHEQGG*GGCGG

Parental  YDHGGRGGGRGNKHQGGWTDGGSASGGGYQDGGYRDPGFQPGGYHGGHSSGYQGGGYGGFQTSSYTGSGY
          YDHGG.GGGRG.KHQGGW.DGGS..GGGYQDGGYRDPGFQPGGYHGGHSSGYQGGG.GGFQTSSY.GSGY
Retrocopy YDHGG*GGGRGKKHQGGWPDGGSGGGGGYQDGGYRDPGFQPGGYHGGHSSGYQGGGDGGFQTSSYRGSGY

Parental  QGGGYQQDNRYQDGGHHGERGSGRGGRGGRGGRGGRGSQGGGWGGRGSQTYH-QGGQFEQHFQHGGYQYS
          QG.GYQQDNRYQDGGHHGE.GSG.GGRGG.GG..G.GSQG.GWGGR..QT.H..GGQFEQHFQHGGYQYS
Retrocopy QGSGYQQDNRYQDGGHHGE*GSGLGGRGG*GGLEGWGSQG*GWGGRRIQT*H<LGGQFEQHFQHGGYQYS

Parental  HSGFGQGRHYTS
          HSGFGQGRH.TS
Retrocopy HSGFGQGRHHTS

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	26.82 RPM
SRP017611_kidney	0.00 RPM	35.80 RPM
SRP017611_liver	0.00 RPM	21.99 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_614 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_614 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_614 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005268	2 retrocopies	retro_amel_1607, retro_amel_1845,
Choloepus hoffmanni	ENSCHOG00000000476	1 retrocopy	retro_chof_691,
Mustela putorius furo	ENSMPUG00000010098	1 retrocopy	retro_mputfur_1193,
Rattus norvegicus	ENSRNOG00000005366	1 retrocopy	retro_rnor_680,
Rattus norvegicus	ENSRNOG00000030328	1 retrocopy	retro_rnor_614 ,