RetrogeneDB ID: retro_rnor_1949

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 4:9810738..9811782(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000029686
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Cryzl1
• Ensembl ID: ENSRNOG00000028014
• Aliases: None
• Description: quinone oxidoreductase-like protein 1 [Source:RefSeq peptide;Acc:NP_001013062]

Sequence

>retro_rnor_1949
ATGAAAGGCTTGTATTTTCAACAGAGTTCTACAAATGAAGAAGTAACATTTGTATTTCAAGAAAAGGAAAATGTCTCTGT
CACAGAGGATAACTTTGTGAGAGTGCAAGTTAAAGCCTGTGCCCTGAGCCACATAAACACAAAGCTTCTAGCAGAGATGA
AGATGGAAAAGGAATTCTTCCCTGTTGGGAGAGAAGTCGCTGGGATTGTATTAGATGTTGGCAAGAAGGTATCGTTCTTT
CAGCCAGATGATGAAGTCGTCGGGATTTTGCCTTTGGATTCGGAAGACCCCGGACTCTGCGAAGTTATCCGAGTACAGGA
GCATTACCTGGTTCATAAGCCAGAAAAGGTGCCATGGACGGAAGCCGCTGGAGTCATCCGGGATGGAGTCCGAGCCTACA
CAGCCCTCTATTACCTTTCTCAGCTCTCTTCCGGGAAGTCCGTGCTGATCATGGATGGGGCAAGTGCATTTGGCACAATA
GCCATTCAGTTAGCACACCACAGAGGAGCCAAGGTGATCTCAACAGCACACAGCCTGGAGGACAAGCAACATCTTGAAAG
GCTTAGGCCTTCTCTAGCCCGAGTGATTGATGTGTCTAGTGGGAAAGTCCATGTTGCTGAAAGGTGCTTGGAAGAAACAG
GTGGCCTGGGAGTAGATATTGTCATAGATGCAGGAGTGAGATTATATAGTAAAGATGATGAACCAGCTGTAAAACAACAA
CTACCACATAAGCATGACATCATCACACTTCTCAGTGTTGGAGGCCATTGGATAACGACAGAAGAAAACCTTCAGTTGGA
TCCTCCAGATAGCCATTGCCTTTTCCTCAAGGGAGCAACAGTGGCTTTCCTTAATGATGAAGTTTGGAATTTGTCAAATG
CACAACAGGGAAAATATCTTTGCATCTGAAAAGACGTGATGGAGAAGCTATCAGCTGGTGTGTTCAGACCTCTGCTTGAT
GAACCCATTCCACTGTATGAGGCCAAAGTTTCCATGGAAGTTGTTCAGAAAAGTCAAGAAAGAAAAAAGCAAGTTGTTCA
ATTT

Alignment

ORF - retro_rnor_1949 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKGLYFQQSSTNEEVTFVFQEKENVSVTEDNFVRVQVKACALSHINTKLLAEMKMEKEFFPVGREVAGIV
          MKGLYFQQSSTNEEVTFVFQEKENVSVTEDNFVRVQVKACALSHINTKLLAEMKMEKEFFPVGREVAGIV
Retrocopy MKGLYFQQSSTNEEVTFVFQEKENVSVTEDNFVRVQVKACALSHINTKLLAEMKMEKEFFPVGREVAGIV

Parental  LDVGKKVSFFQPDDEVVGILPLDSEDPGLCEVIRVQEHYLVHKPEKVPWTEAAGVIRDGVRAYTALYYLS
          LDVGKKVSFFQPDDEVVGILPLDSEDPGLCEVIRVQEHYLVHKPEKVPWTEAAGVIRDGVRAYTALYYLS
Retrocopy LDVGKKVSFFQPDDEVVGILPLDSEDPGLCEVIRVQEHYLVHKPEKVPWTEAAGVIRDGVRAYTALYYLS

Parental  QLSPGKSVLIMDGASAFGTIAIQLAHHRGAKVISTAHSLEDKQHLERLRPSLARVIDVSSGKVHVAERCL
          QLS.GKSVLIMDGASAFGTIAIQLAHHRGAKVISTAHSLEDKQHLERLRPSLARVIDVSSGKVHVAERCL
Retrocopy QLSSGKSVLIMDGASAFGTIAIQLAHHRGAKVISTAHSLEDKQHLERLRPSLARVIDVSSGKVHVAERCL

Parental  EETGGLGVDIVIDAGVRLYSKDDEPAVKQQLPHKHDIITLLSVGGHWITTEENLQLDPPDSHCLFLKGAT
          EETGGLGVDIVIDAGVRLYSKDDEPAVKQQLPHKHDIITLLSVGGHWITTEENLQLDPPDSHCLFLKGAT
Retrocopy EETGGLGVDIVIDAGVRLYSKDDEPAVKQQLPHKHDIITLLSVGGHWITTEENLQLDPPDSHCLFLKGAT

Parental  VAFLNDEVWNLSNAQQGKYLCILKDVMEKLSAGVFRPLLDEPIPLYEAKVSMEVVQKSQERKKQVVQF
          VAFLNDEVWNLSNAQQGKYLCI.KDVMEKLSAGVFRPLLDEPIPLYEAKVSMEVVQKSQERKKQVVQF
Retrocopy VAFLNDEVWNLSNAQQGKYLCI*KDVMEKLSAGVFRPLLDEPIPLYEAKVSMEVVQKSQERKKQVVQF

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	22.00 RPM
SRP017611_kidney	0.00 RPM	6.70 RPM
SRP017611_liver	0.00 RPM	2.96 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1949 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1949 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1949 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Otolemur garnettii	ENSOGAG00000015836	1 retrocopy	retro_ogar_848,
Rattus norvegicus	ENSRNOG00000028014	1 retrocopy	retro_rnor_1949 ,