RetrogeneDB ID: retro_rnor_88

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 12:35899611..35900388(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000000964
• Aliases: Frg1l1, Frg1
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Frg1
• Ensembl ID: ENSRNOG00000009846
• Aliases: None
• Description: None

Sequence

>retro_rnor_88
ATGGCCGAATATTCTTACGTAAAGTCCACCAAACTCGTGCTCAAGGGCACTAAAGCCAAGAGTAAAAAGAAAAAGAGCAA
AGATAAGAAGAGAAAACGAGAAGAAGACGAGGAAGCGCAACTTGACATTGTGGGAATCTGGTGGACTGTATCCAATTTCG
GTGAGATTTCAGGAACCATTGCCATTGAAATGGATAAAGGAGCCTATATCCATGCACTGGACAATGGCCTCTTTACACTG
GGAGCGCCACACAGAGAAGTCGATGAGGGCTCCAGTCCTCCAGAGCAGTTTACTGCCGTTAAATTGTCTGATTCCAGAAT
TGCCCTGAAGTCTGGCTATGGAAAATATCTCGGTATAAATTCAGATGGACTTGTTGTTGGGCGTTCAGATGCAATTGGGC
CAAGAGAACAATGGGAACCAGTGTTTCAAGATGGGAAGATGGCTTTACTGGCCTCAAATAGCTGCTTTATTAGATGTAAT
GAAGCAGGCGATATAGAAGCAAAGAATAAAACAGCAGGAGAAGAAGAAATGATAAAGATCAGATCCTGTGCGGAAAGAGA
AGCCAAGAAGAAGGACGACATCGCAGAGGAAGACAAGGGAAGCGTGCAGCAGTGTGAGATCAACTATGTAAAGAAATTTC
AGAGCTTCCAAGACCATAAACTCAAAATAAGCAAAGAAGATAGTAAAATTCTTAAAAAGGCTCGGAAAGATGGATTTTTG
CACGAGACCCTTCTGGACAGGAGAGCCAAATTGAAAGCCGACCGATATTGCAAGTGA

Alignment

ORF - retro_rnor_88 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.85 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEYSYVKSTKLVLKGTKAKSKKKKSKDKKRKREEDEEAQLDIVGIWWTVSNFGEISGTIAIEMDKGAYI
          MAEYSYVKSTKLVLKGTKAKSKKKKSKDKKRKREEDEEAQLDIVGIWWTVSNFGEISGTIAIEMDKGAYI
Retrocopy MAEYSYVKSTKLVLKGTKAKSKKKKSKDKKRKREEDEEAQLDIVGIWWTVSNFGEISGTIAIEMDKGAYI

Parental  HALDNGLFTLGAPHREVDEGPSPPEQFTAVKLSDSSQRIALKSGYGKYLGINSDGLVVGRSDAIGPREQW
          HALDNGLFTLGAPHREVDEG.SPPEQFTAVKLSDS..RIALKSGYGKYLGINSDGLVVGRSDAIGPREQW
Retrocopy HALDNGLFTLGAPHREVDEGSSPPEQFTAVKLSDS--RIALKSGYGKYLGINSDGLVVGRSDAIGPREQW

Parental  EPVFQDGKMALLASNSCFIRCNEAGDIEAKNKTAGEEEMIKIRSCAEREAKKKDDIAEEDKGSVQQCEIN
          EPVFQDGKMALLASNSCFIRCNEAGDIEAKNKTAGEEEMIKIRSCAEREAKKKDDIAEEDKGSVQQCEIN
Retrocopy EPVFQDGKMALLASNSCFIRCNEAGDIEAKNKTAGEEEMIKIRSCAEREAKKKDDIAEEDKGSVQQCEIN

Parental  YVKKFQSFQDHKLKISKEDSKILKKARKDGFLHETLLDRRAKLKADRYCK
          YVKKFQSFQDHKLKISKEDSKILKKARKDGFLHETLLDRRAKLKADRYCK
Retrocopy YVKKFQSFQDHKLKISKEDSKILKKARKDGFLHETLLDRRAKLKADRYCK

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	0.72 RPM	7.98 RPM
SRP017611_kidney	0.49 RPM	7.68 RPM
SRP017611_liver	0.74 RPM	4.98 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_88 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_88 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_88 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013503	1 retrocopy	retro_amel_1609,
Canis familiaris	ENSCAFG00000007135	1 retrocopy	retro_cfam_718,
Cavia porcellus	ENSCPOG00000022277	7 retrocopies	retro_cpor_1349, retro_cpor_1350, retro_cpor_1359, retro_cpor_1361, retro_cpor_1362, retro_cpor_1363, retro_cpor_864,
Felis catus	ENSFCAG00000025737	1 retrocopy	retro_fcat_464,
Myotis lucifugus	ENSMLUG00000023179	2 retrocopies	retro_mluc_1185, retro_mluc_1490,
Otolemur garnettii	ENSOGAG00000005749	2 retrocopies	retro_ogar_1523, retro_ogar_2535,
Pan troglodytes	ENSPTRG00000016671	1 retrocopy	retro_ptro_2930,
Rattus norvegicus	ENSRNOG00000009846	1 retrocopy	retro_rnor_88 ,
Sorex araneus	ENSSARG00000002471	1 retrocopy	retro_sara_368,
Tupaia belangeri	ENSTBEG00000014491	2 retrocopies	retro_tbel_1202, retro_tbel_3435,
Tarsius syrichta	ENSTSYG00000010985	2 retrocopies	retro_tsyr_1347, retro_tsyr_1778,