RetrogeneDB ID: retro_rnor_2379

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:89653622..89654558(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CYP51A1
• Ensembl ID: ENSRNOG00000007234
• Aliases: Cyp51, Cyp51a1, RATCP14DM
• Description: Lanosterol 14-alpha demethylase [Source:UniProtKB/Swiss-Prot;Acc:Q64654]

Sequence

>retro_rnor_2379
ATGGTACTGCTGGGCTTGCTGCAGTCAGGCGGCTCGGTGCTCGGGCAGGCGATGGAGCAGGTGACAGGAGGCAACCTGCT
TTCCACGCTGCTCATCGCCTGCGCCTTCACGCTCAGCCTTGTCTACCTGTTCCGCCTCGCAGTGGGCCACATGGTCCAGC
TGCCCGCTGGAGCGGAAAGTCCGCCATGTATTTACTCTCCAATTCCGTTCCTTGGCCATGCGATAGCGTTTGGAAAAAGT
CCAATTGAGTTCCTGGAAAATGCATATGAGAAGTCCGGACCTGTGTTTAGCTTTACCATGGTGGGCAAGACCTTCACTTA
CCTTTTGGGGAGCGATGCAGCCGCACTGCTCTTCAACAGTAAGAACGAAGACCTGAATGCGGAAGAAGTCTACGGTCGGC
TGACAACACCCGTGTTTGGGAAGGGAGTTGCATACGATGTGCCAAATGCAGTTTTCCTGGAACACAAGAAAATACTAAAA
AGCGGCCTTAACATAGCCCACTTCAAGCAGTATGTTTCTATCACTGAAAAAGAAGCGAAGGAGTACTTTAAAAGTTGGGG
AGAAAGCGGAGAAAGAAATGTGTTTGAAGCGCTGTCTGAGCTCATAATTTTAACAGCTAGCCATTGTTTACACGGAAAGG
AAATTAGGAGTCAACTCAACGAGAAGGTGGCTCAGCTGTATGCAGACCTGGATGGAGGCTTTAGCCACGCTGCCTGGCTG
TTGCCAGGTTGGCTGCCTCTGCCAAGTTTCAGGCGCAGGGACAGAGCCCATCGAGAGATCAAGAATATTTTCTACAAGGC
CATCCAGAAACGTAGGCTGTCAAAAGAACCAGCCGAGGACATTCTTCAAACTTTACTGGATTCTACATACAAGGATGGGC
GTCCTCTGACAGACGACGTGATAGCAGGGATGCTCATCGGACTGCTGCTGGCCGGA

Alignment

ORF - retro_rnor_2379 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.08 %
• Parental protein coverage: 62.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVLLGLLQSGGSVLGQAMEQVTGGNLLSTLLIACAFTLSLVYLFRLAVGHMVQLPAGAKSPPYIYSPIPF
          MVLLGLLQSGGSVLGQAMEQVTGGNLLSTLLIACAFTLSLVYLFRLAVGHMVQLPAGA.SPP.IYSPIPF
Retrocopy MVLLGLLQSGGSVLGQAMEQVTGGNLLSTLLIACAFTLSLVYLFRLAVGHMVQLPAGAESPPCIYSPIPF

Parental  LGHAIAFGKSPIEFLENAYEKYGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEEVYGRLTTPVFG
          LGHAIAFGKSPIEFLENAYEK.GPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEEVYGRLTTPVFG
Retrocopy LGHAIAFGKSPIEFLENAYEKSGPVFSFTMVGKTFTYLLGSDAAALLFNSKNEDLNAEEVYGRLTTPVFG

Parental  KGVAYDVPNAVFLEQKKILKSGLNIAHFKQYVSIIEKEAKEYFKSWGESGERNVFEALSELIILTASHCL
          KGVAYDVPNAVFLE.KKILKSGLNIAHFKQYVSI.EKEAKEYFKSWGESGERNVFEALSELIILTASHCL
Retrocopy KGVAYDVPNAVFLEHKKILKSGLNIAHFKQYVSITEKEAKEYFKSWGESGERNVFEALSELIILTASHCL

Parental  HGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKNIFYKAIQKRRLSKEPAED
          HGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKNIFYKAIQKRRLSKEPAED
Retrocopy HGKEIRSQLNEKVAQLYADLDGGFSHAAWLLPGWLPLPSFRRRDRAHREIKNIFYKAIQKRRLSKEPAED

Parental  ILQTLLDSTYKDGRPLTDDEIAGMLIGLLLAG
          ILQTLLDSTYKDGRPLTDD.IAGMLIGLLLAG
Retrocopy ILQTLLDSTYKDGRPLTDDVIAGMLIGLLLAG

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	120.57 RPM
SRP017611_kidney	0.00 RPM	30.63 RPM
SRP017611_liver	0.13 RPM	188.87 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2379 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2379 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000011496	1 retrocopy	retro_ggor_1952,
Monodelphis domestica	ENSMODG00000010610	1 retrocopy	retro_mdom_436,
Rattus norvegicus	ENSRNOG00000007234	1 retrocopy	retro_rnor_2379 ,