RetrogeneDB ID: retro_rnor_2124

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:1313293..1314212(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Fam149b1
• Ensembl ID: ENSRNOG00000006554
• Aliases: Fam149b1, RGD1359592
• Description: Protein FAM149B1 [Source:UniProtKB/Swiss-Prot;Acc:Q5PQL8]

Sequence

>retro_rnor_2124
AACCGCACAGATATGGAAGAAGGATTTCATGGAAACAAATCAGAAGCAGCTACAGAGAAACAGAAGTTAGGGTACCCTCC
CATTGCACCATTTTACTGCATGAAAGAGGATGTTCTTGCTTATGTGTTTGACAATGTGTGGAACAAGGTTGTGGGCTGTA
TGGAGCAGTTGACACATAGTCACTGGGAGGGATGTGCCTCTGATGATGAGAGTAACAGTGAAATTATCAGACTAGATTCA
GGAAGTCCCTATGTGCTGAACGAACAGACCCTTTGGTCTTATTCAAGTGCAGCAGTATGAGGTGCTGTCAATCACCTCAA
ATCCAATGTGTTTCTGTCAAGCAAGTAGTCATCAACTGAACATGAATGGTCTCTTGATTCATGGGATGTCTCTACAGCCA
AGGAATTCTCTCTGATGGATAAGCTCCTAGATCTTGATGACAAGCTACTCACGAGGCCTGGGTCCAATTCCATCCTTTCA
AACCACAATTGGCCAAACCAAGCCATGGAGCTCAATATGTCATCTTTGTCATATACAAAGTGATCTGCCAGGAGGCGCAA
TCCCCCACCACATACCCTTCATCCGATCAGCACAAGCCACGCACATGCTGGAACACCATGGTCTGCAGAAGAAGTCCTCA
GAGGACCCTGGGTTCCAGTGACAGCAGATACACTCTCTTCTCTCTCACCAATGACCTTGAATCAGAACAATCTGTTGCCA
CCTATCGGAACAGCTGAAGTAGAACACCTGAGCACCATGGGGGCTACAAAAGCCAACAAAATCCCATGGTGACTCCACCT
GAGCCCAAAGTACAATGGTGTACGAGCCTAGCCAGCAGCCCCAGGAGAGGCTCCTTTTGCCTGTCTTCTCTAGACCCAAC
ACAACTCAGTCATTTTTGCCAGACACACTGTACATGTCT

Alignment

ORF - retro_rnor_2124 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.78 %
• Parental protein coverage: 63.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DHTDMEEGFHGNKSEAATEKQKLGYPPIAPFYCMKEDVLAYVFDNVWSKAVGCMEQLTRSHWEGFASDDE
          ..TDMEEGFHGNKSEAATEKQKLGYPPIAPFYCMKEDVLAYVFDNVW.K.VGCMEQLT.SHWEG.ASDDE
Retrocopy NRTDMEEGFHGNKSEAATEKQKLGYPPIAPFYCMKEDVLAYVFDNVWNKVVGCMEQLTHSHWEGCASDDE

Parental  SNVEITRLDSGSPYMLNEQ-QPLVLPR-VPQSKVMSVTSNPMNFCQASGHQPNVNGLLIHGMPLQPRN-L
          SN.EI.RLDSGSPY.LNEQ..PLVL...V.Q..V.S.TSNPM.FCQAS.HQ.N.NGLLIHGM.LQPRN..
Retrocopy SNSEIIRLDSGSPYVLNEQ<DPLVLFK<VQQYEVLSITSNPMCFCQASSHQLNMNGLLIHGMSLQPRN<F

Parental  SLMDKLLDLDDKLLMRPGSSSVLSNRNWPNRAMELSTSSLSYTTQSARRRNPPPRTLHPISTSHSRTGTP
          SLMDKLLDLDDKLL.RPGS.S.LSN.NWPN.AMEL..SSLSYT..SARRRNPPP.TLHPISTSH...GTP
Retrocopy SLMDKLLDLDDKLLTRPGSNSILSNHNWPNQAMELNMSSLSYTK*SARRRNPPPHTLHPISTSHAHAGTP

Parental  WPAEEILRGPRLPMTADSLSSPSPMTMGRNNLLPPIGTADVEHLSILGS-QRPTKPHGDSSRARSAAVDE
          W.AEE.LRGP..P.TAD.LSS.SPMT...NNLLPPIGTA.VEHLS..G..Q.PTK.HGDS..A.S..V.E
Retrocopy WSAEEVLRGPWVPVTADTLSSLSPMTLNQNNLLPPIGTAEVEHLSTMGA>QKPTKSHGDST*AQSTMVYE

Parental  PNQQPQERLLLPVFSRPNTTQSFLPETQYRS
          P.QQPQERLLLPVFSRPNTTQSFLP.T.Y.S
Retrocopy PSQQPQERLLLPVFSRPNTTQSFLPDTLYMS

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	0.14 RPM	35.59 RPM
SRP017611_kidney	0.00 RPM	35.87 RPM
SRP017611_liver	0.00 RPM	17.55 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2124 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2124 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138286	1 retrocopy	retro_hsap_1529,
Macaca mulatta	ENSMMUG00000011281	1 retrocopy	retro_mmul_2158,
Nomascus leucogenys	ENSNLEG00000016575	1 retrocopy	retro_nleu_1938,
Pan troglodytes	ENSPTRG00000002623	2 retrocopies	retro_ptro_1036, retro_ptro_2950,
Rattus norvegicus	ENSRNOG00000006554	1 retrocopy	retro_rnor_2124 ,
Ictidomys tridecemlineatus	ENSSTOG00000002142	1 retrocopy	retro_itri_429,