RetrogeneDB ID: retro_rnor_2676

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 9:38638814..38640202(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000024624
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zfp622
• Ensembl ID: ENSRNOG00000049087
• Aliases: Zfp622, Znf622
• Description: zinc finger protein 622 [Source:RefSeq peptide;Acc:NP_001009652]

Sequence

>retro_rnor_2676
ATGGCGACGTACACCTGCATCACCTGCCGGGTGGCGTTCCGCGATGCGGAGATGCAGCGGGCTCACTACAAGACCGACTG
GCACCGCTACAACCTGCGGCACAAGGTGGCTAATATGGCCCCGGTGACCGCCGAAGGCTTCCAGGAGCGGGTGCGAGCGC
AGCGGGCGGTGGCGGAGGAGGAGAGCAAGGGCACGGCCACCGTGTGCAGCAAGAAGTTCGCCACGTTCAACGCCTACGAG
AACTACCTTAAGTCCCGGCTGCACGTGGAGCTGGAGAAGAAGACGGTGCAGGCCGTGAGCCGCCAAGTGGAGATGATGAA
CGAGAAGAACTTGGAGAAGGGACTGGGCGTGGACAGTGTGAACAAGGATGCCATGAACGCCGCCATCCAGCAGGCCATCA
AGGCCCAGCCTTCCACGTCTCCCAAGAAAGCGCCCTTCATGCCCACGGACGAATCCAGGAGGGTGGCGGGCGCGGTCCGA
CGGGGCACCCGGGAGCAAGACCCGACGGAGAAGCCGCCCTGGCTCCAGTGGTTCGAACAGCAGGAGAAGAAGCTGGCGAA
GCAGCAGTGGGAGGAGAGTGAGGAAGAGGGAGAGGAAGACGACGAAGATTGGGAAGATATTGATTCCGATGATGGATTGG
AATGTGAGAACCCTGGAGTGGAGGAAGAGGATGCAGAAGATGCAGAGGCTGAGGAGAGCCCACCCCTAGGTGCCATCCCA
ATAACAGACTGCTTATTTTGTTCCCATCATTCAAGCTCCCTTGTGAAGAATGTGGCTCATATGACTAAAGTCCACAGCTT
TTTTATTCCTGATATAGAGTATCTTTCAGATTTGAAAGGATTAATTAAATATTTGGGAGAGAAAGTTGGTGCTGGCAAAA
TCTGCTTGTGGTGCAATGAGAAAGGGAAGTCCTTCTATTCCACAGAAGCTGTGCAGGCACACATGAATGACAAAAGCCAC
TGTAAGCTCTTTACAGATGGTGATGCTGTGCTGGAGTTTGCAGACTTCTATGATTTTAGGAGTAGCTACCCAGATTACAA
GGAGGGGCAGGATCCTGCTGAGATTGAAGACTTGTCCTTGGAATGTGATGATGAAACCATGGAGCTGATAATTCCCTCTG
GTGCCAGGGTGGGTCATCGCTCCTTGATGAGATACTACAAACAACGATTTGGCTTGCCAAGAGCTGTGACAGTTGCTAGA
AATCAAAAGGCTGTGGGCAGGGTCCTCCAGCAGTACCGAGCCCTGGGGTGGACGGGCAGCACAGGAGCAGCTCTCATGCG
TGAACGGGATATGCAGTATGTACAGAGGTGAAGTCGAAATGGATGCTGAAGACCGGGATGAAGAACAATGCCACCAAGCA
GATGCACTTTAGGGCCCAAGTGAGATTC

Alignment

ORF - retro_rnor_2676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.75 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATYTCITCRVAFRDAEMQRAHYKTDWHRYNLRRKVANMAPVTAEGFQERVRAQRAVAEEESKGTATYCT
          MATYTCITCRVAFRDAEMQRAHYKTDWHRYNLR.KVANMAPVTAEGFQERVRAQRAVAEEESKGTA...T
Retrocopy MATYTCITCRVAFRDAEMQRAHYKTDWHRYNLRHKVANMAPVTAEGFQERVRAQRAVAEEESKGTA---T

Parental  VCSKKFATFNAYENHLKSRRHVELEKKAVQAVSRQVEMMNEKNLEKGLGVDSVNKDAMNAAIQQAIKAQP
          VCSKKFATFNAYEN.LKSR.HVELEKK.VQAVSRQVEMMNEKNLEKGLGVDSVNKDAMNAAIQQAIKAQP
Retrocopy VCSKKFATFNAYENYLKSRLHVELEKKTVQAVSRQVEMMNEKNLEKGLGVDSVNKDAMNAAIQQAIKAQP

Parental  STSPKKAPFMPTDESRRVAGAVRRGTPERDPTEKPPRLQWFEQQAKKLAKQQWEESEEEGEEDDEDWEDI
          STSPKKAPFMPTDESRRVAGAVRRGT.E.DPTEKPP.LQWFEQQ.KKLAKQQWEESEEEGEEDDEDWEDI
Retrocopy STSPKKAPFMPTDESRRVAGAVRRGTREQDPTEKPPWLQWFEQQEKKLAKQQWEESEEEGEEDDEDWEDI

Parental  DSDDGLECENPGVEEEDAEDAEAEESPPLGAIPITDCLFCSHHSSSLVKNVAHMTKVHSFFIPDIEYLSD
          DSDDGLECENPGVEEEDAEDAEAEESPPLGAIPITDCLFCSHHSSSLVKNVAHMTKVHSFFIPDIEYLSD
Retrocopy DSDDGLECENPGVEEEDAEDAEAEESPPLGAIPITDCLFCSHHSSSLVKNVAHMTKVHSFFIPDIEYLSD

Parental  LKGLIKYLGEKVGVGKICLWCNEKGKSFYSTEAVQAHMNDKSHCKLFTDGDAALEFADFYDFRSSYPDYK
          LKGLIKYLGEKVG.GKICLWCNEKGKSFYSTEAVQAHMNDKSHCKLFTDGDA.LEFADFYDFRSSYPDYK
Retrocopy LKGLIKYLGEKVGAGKICLWCNEKGKSFYSTEAVQAHMNDKSHCKLFTDGDAVLEFADFYDFRSSYPDYK

Parental  EGQDPAEIEDLSSEKILECDDETMELILPSGARVGHRSLMRYYKQRFGLPRAVTVARNQKAVGRVLQQYR
          EGQDPAEIEDLS....LECDDETMELI.PSGARVGHRSLMRYYKQRFGLPRAVTVARNQKAVGRVLQQYR
Retrocopy EGQDPAEIEDLS----LECDDETMELIIPSGARVGHRSLMRYYKQRFGLPRAVTVARNQKAVGRVLQQYR

Parental  ALGWTGSTGAALMRERDMQYVQR-MKSKWMLKTGMKNNATKQMHFRAQVRF
          ALGWTGSTGAALMRERDMQYVQR..KSKWMLKTGMKNNATKQMHFRAQVRF
Retrocopy ALGWTGSTGAALMRERDMQYVQR<VKSKWMLKTGMKNNATKQMHFRAQVRF

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	9.92 RPM
SRP017611_kidney	0.00 RPM	6.70 RPM
SRP017611_liver	0.00 RPM	3.70 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2676 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2676 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2676 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012047	1 retrocopy	retro_cjac_4226,
Rattus norvegicus	ENSRNOG00000049087	1 retrocopy	retro_rnor_2676 ,
Tupaia belangeri	ENSTBEG00000006779	1 retrocopy	retro_tbel_1283,