RetrogeneDB ID: retro_rnor_384

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:74412254..74414036(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000046832
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ccdc41
• Ensembl ID: ENSRNOG00000007859
• Aliases: Ccdc41, Cep83, RGD1359593
• Description: Coiled-coil domain-containing protein 41 [Source:UniProtKB/Swiss-Prot;Acc:Q66H89]

Sequence

>retro_rnor_384
ATGGACACATTTCCTAGCATATTTCCACCCGGAGGAGACAGTAGGCTGAATCCTGAACCTGAGTTCCAAAGTATGTTAAT
AGATGAAAGGGTACGATGTGAACATCATAAACATAATTATCAGGCTCTGAAAATTGAACACAAAAGGTTGCAGGAAAAAT
ATGTAAAATCACAAAATGAACTTAAGCGTGTGTTAAATGAAAAACAAACAAACCAGGAAAAATTCCAACTGCTCCTTGAA
GAGTTAAGGGGGGAATTAGTAGAGAAAGTTAAGGACATGGAAGCAATGAAACTGCAGATATTAACACCACAAAAATTGGA
ATTGGTAAAAGCCCAACTACAACAAGAATTAGAAGCTCCAATGCGAGAACGTTTTCGGACTCTTGATGAAGAAGTGGAAA
GGTACAGAGCTGAGTACAACAAGCTCCGCTACGAGCACACATTCCTCAAGTCAGAGTTTGAACACCAGAAGGAAGAGCTT
ACTCGTATTGCAGAAGAAGAAAAAATGAAATACAAGTCAGAGGTTGCACGACTGGAGAAGGATAAAGAGGAACTACATAA
CCAGCTGCTTAGTGTTGATCCCACAAGAGATAGCAAACGAGTGGAGCAACTTGTTCGAGAAAAAACCCATTTGCTTCAGA
AATTGAAAAGTTTAGAGGCTGAAGTAGCAGAATTAAGGGCTGAGAAAGAGAATTCTGGTGCTCAGGTAGAAAATGTCCAA
AGAATACAAGTGAGGCAGTTGGCTGAGATGCAGGCCACTCTCAGATCCTTGGAGGCTGAAAAGCAGTCAGCTAAACTACA
GGCTGAACGCCTAGAAAAAGAGCTACAATCAAGCAACGAACAAAACACCTGTTTAATTAGTAAATTGCATAAGGCTGACC
GAGAAATAAGCACGCTGACTAGTCAGGTGAAAGAGCTTAAACATGCAAACAAGCTCGAAATAACTGACGTCAAACTGGAG
GCTGCAAGAGCGAAGAGTGAGCTAGAGCGAGAGAGGAATAAGATCCAAAGTGAACTCGATGGACTGCAGTCAGACAATGA
AATTCTCAAGTCGACTGTTGAACACCACAAAGTGCTCTTGGTGGAAAAAGATCGTGAATTAATACGTAAAGTACAAGCTG
CCAAGGAAGAAGGTTACCAGAAACTTGTGGTCTTGCAAGATGAAAAGCTAGAACTTGAGAACAGATTATCAGACTTAGAG
AAAATGAAAGTGGAGCATGATGTCTGGAGGCAGTCGGAAAAGGATCAGTGTGAAGAGAAGCTGCGGGCCTCCCAGGCGGC
AGAGGAGGCAGCCCGGAGGGAACTGCAGAGCATTAGGTTAAAACTTCAACAACAAATTGTGAATACCGAAAAAGCAGAGA
AAGAAAAACTTGAAAATTCTGAACTGAAACAGCAAATCAGTCATTTACAGATCCAAGTGACCTCACTGACGCAGTCAGAG
AATGACTTGCTGAATTCAAACCAAATGCTGAAGGACATGGTGGAGAGGTTAAAGCAAGAGTGCCGACATTTAAGAAGCCA
AGCTGAAAAAGTGCAACTAGAAGTTGAAAAGACACTGGAGGAAAAGCAGATACAGTGGTTGGAAGAAAAGCATAAGCTTC
ATGAGCGTATCACAGACAGAGAGGAAAAGTACAATCAAGCAAAAGAGAAACTGCAGCGGGCAGCAACTGCTCAGAAAAAG
AGAAAATCTCTTCATGAGAATAAATTGAAGAGACTGCAGGAGAAAGTGGAAGTCTTGGAGGCAAAGAAAGAAGAATTAGA
GACAGAAAACCAGGTGTTAAAT

Alignment

ORF - retro_rnor_384 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.66 %
• Parental protein coverage: 85.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTFPSIFPPGGDSRLNPEPEFQSMLIDERVRCEHHKHNYQALKIEHKRLQEEYVKSQNELKRVLNEKQT
          MDTFPSIFPPGGDSRLNPEPEFQSMLIDERVRCEHHKHNYQALKIEHKRLQE.YVKSQNELKRVLNEKQT
Retrocopy MDTFPSIFPPGGDSRLNPEPEFQSMLIDERVRCEHHKHNYQALKIEHKRLQEKYVKSQNELKRVLNEKQT

Parental  NQEKFQLLLEELRGELVEKVKDMEAMKLQILTPQKLELVKAQLQQELEAPMRERFRTLDEEVERYRAEYN
          NQEKFQLLLEELRGELVEKVKDMEAMKLQILTPQKLELVKAQLQQELEAPMRERFRTLDEEVERYRAEYN
Retrocopy NQEKFQLLLEELRGELVEKVKDMEAMKLQILTPQKLELVKAQLQQELEAPMRERFRTLDEEVERYRAEYN

Parental  KLRYEHTFLKSEFEHQKEELTRISEEEKMKYKSEVARLEKDKEELHNQLLSVDPTRDSKRVEQLVREKTH
          KLRYEHTFLKSEFEHQKEELTRI.EEEKMKYKSEVARLEKDKEELHNQLLSVDPTRDSKRVEQLVREKTH
Retrocopy KLRYEHTFLKSEFEHQKEELTRIAEEEKMKYKSEVARLEKDKEELHNQLLSVDPTRDSKRVEQLVREKTH

Parental  LLQKLKSLEAEVAELRAEKENSGAQVENVQRIQVRQLAEMQATLRSLEAEKQSAKLQAERLEKELQSSNE
          LLQKLKSLEAEVAELRAEKENSGAQVENVQRIQVRQLAEMQATLRSLEAEKQSAKLQAERLEKELQSSNE
Retrocopy LLQKLKSLEAEVAELRAEKENSGAQVENVQRIQVRQLAEMQATLRSLEAEKQSAKLQAERLEKELQSSNE

Parental  QNTCLISKLHKADREISTLTSQVKELKHANKLEITDVKLEAARAKSELERERNKIQSELDGLQSDNEILK
          QNTCLISKLHKADREISTLTSQVKELKHANKLEITDVKLEAARAKSELERERNKIQSELDGLQSDNEILK
Retrocopy QNTCLISKLHKADREISTLTSQVKELKHANKLEITDVKLEAARAKSELERERNKIQSELDGLQSDNEILK

Parental  STVEHHKVLLVEKDRELIRKVQAAKEEGYQKLVVLQDEKLELENRLSDLEKMKVEHDVWRQSEKDQCEEK
          STVEHHKVLLVEKDRELIRKVQAAKEEGYQKLVVLQDEKLELENRLSDLEKMKVEHDVWRQSEKDQCEEK
Retrocopy STVEHHKVLLVEKDRELIRKVQAAKEEGYQKLVVLQDEKLELENRLSDLEKMKVEHDVWRQSEKDQCEEK

Parental  LRASQAAEEAARRELQSIRLKLQQQIVNTEKAEKEKLENSELKQQISHLQIQVTSLTQSENDLLNSNQML
          LRASQAAEEAARRELQSIRLKLQQQIVNTEKAEKEKLENSELKQQISHLQIQVTSLTQSENDLLNSNQML
Retrocopy LRASQAAEEAARRELQSIRLKLQQQIVNTEKAEKEKLENSELKQQISHLQIQVTSLTQSENDLLNSNQML

Parental  KDMVERLKQECRHLRSQAEKVQLEVEKTLEEKQIQWLEEKHKLHERITDREEKYNQAKEKLQRAATAQKK
          KDMVERLKQECRHLRSQAEKVQLEVEKTLEEKQIQWLEEKHKLHERITDREEKYNQAKEKLQRAATAQKK
Retrocopy KDMVERLKQECRHLRSQAEKVQLEVEKTLEEKQIQWLEEKHKLHERITDREEKYNQAKEKLQRAATAQKK

Parental  RKSLHENKLKRLQEKVEVLEAKKEELETENQVLN
          RKSLHENKLKRLQEKVEVLEAKKEELETENQVLN
Retrocopy RKSLHENKLKRLQEKVEVLEAKKEELETENQVLN

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	1.87 RPM	30.41 RPM
SRP017611_kidney	0.42 RPM	11.72 RPM
SRP017611_liver	0.20 RPM	5.65 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_384 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_384 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_384 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009750	1 retrocopy	retro_amel_1376,
Callithrix jacchus	ENSCJAG00000002860	1 retrocopy	retro_cjac_1662,
Cavia porcellus	ENSCPOG00000008997	1 retrocopy	retro_cpor_1537,
Rattus norvegicus	ENSRNOG00000007859	1 retrocopy	retro_rnor_384 ,