RetrogeneDB ID: retro_ocun_811

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 15:81224307..81225396(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000026998
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NR5A2
• Ensembl ID: ENSOCUG00000006240
• Aliases: None
• Description: nuclear receptor subfamily 5, group A, member 2 [Source:HGNC Symbol;Acc:7984]

Sequence

>retro_ocun_811
AGAAGAAAGCCCTCATCCGCGCTAACGGCTAACGGACTGAAGCTGGAAGCCATGTCGCAGGTGATCCAGGCCATGCCCTC
TGAGTTGAGCATCTCCTCTGCGATCCAGAACACGCACTCTGCCTCCAAAGGCCTACCTCTGAACCACGCTGCCTTGCCTC
CCTCAGACTACGACAGAAGTCCCTTTGTCACCTCCCCCATTAGCATGACAATGCCACCTCCTGGCAGCCTGCAAGGTTAC
CAAGCATATGGCCACTTTCCGAGCCGGGCTATCAAGTCTGAGTACCCGGACCCCTACAGCAGCTCTCCCGAGTCCATCCT
AGGCTACTCCTACGTGGACAGCTACCAGACCGGCTCCCCGGCCAGCATCCCGCAGCTCATCCTGGAACTTCTGAAGTGCG
AGCCGGAGGAGCCGCAGGTGCAGGCCAGGATCATGGCCTACTTGCAGCAGGAGCAGGCCAACCGGAGCAAGCACGAGAAG
CTGAGCACATTCGGGCTGATGTGCAAGATGGCGGACCAGACGCTCTTCTCCATCGTGGAGTGGGCCAGGAGTAGTATTTT
CTTCAGAGAACTTAAGGTTGACGACCAAATGAAGCTGCTTCAGAACTGTTGGAGTGAGCTCCTAATCCTGGACCACATTT
ACCGGCAGGTGGTGCACGGGAAGGAAGGATCCATCTACCTGGTTACTGGACAACAAGTGGACCACTCCATAATAACAGCA
CAAGCAGGTGCCACGCTCAACAACCTCATGAGTCATGCCCAGGAGTTGGTGGTAAAACTTCGCTCTCTCCAGTTTGATCA
ACGGGAATTTGTGTGTCTGAAATTCTTGGTGCTCTTTAGTTTAGATGTCAAAAATCTTGAGAACTTCCAGCTGGTAGAAG
GTGTTCAGGAACAAGTGAACGCTGCCCTCCTGGACTACACCATGTGTAACTACCCGCAGCAGACAGAGAAGTTCGGGCAG
CTCCTGCTGCGACTTCCGGAAATCCGGGCCATCAGCATGCAAGCTGAAGAATACCTCTACTACAAGCACCTGAACGGGGA
CGTGCCCTACAATAACCTCCTCATTGAGATGCTGCATGCGAAAAGAGCC

Alignment

ORF - retro_ocun_811 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.97 %
• Parental protein coverage: 67.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KQQKKALIRANGLKLEAMSQVIQAMPSELSISSAIQNMHSASKGLPLNHAALPPSDYDRSPFVTSPISMT
          .........ANGLKLEAMSQVIQAMPSELSISSAIQN.HSASKGLPLNHAALPPSDYDRSPFVTSPISMT
Retrocopy RRKPSSALTANGLKLEAMSQVIQAMPSELSISSAIQNTHSASKGLPLNHAALPPSDYDRSPFVTSPISMT

Parental  MPPPGSLQGYQAYGHFPSRAIKSEYPDPYSSSPESILGYSYVDSYQTGSPASIPQLILELLKCEPEEPQV
          MPPPGSLQGYQAYGHFPSRAIKSEYPDPYSSSPESILGYSYVDSYQTGSPASIPQLILELLKCEPEEPQV
Retrocopy MPPPGSLQGYQAYGHFPSRAIKSEYPDPYSSSPESILGYSYVDSYQTGSPASIPQLILELLKCEPEEPQV

Parental  QARIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLIL
          QARIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLIL
Retrocopy QARIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLIL

Parental  DHIYRQVVHGKEGSIYLVTGQQVDHSIIAAQAGATLNNLMSHAQELVVKLRSLQFDQREFVCLKFLVLFS
          DHIYRQVVHGKEGSIYLVTGQQVDHSII.AQAGATLNNLMSHAQELVVKLRSLQFDQREFVCLKFLVLFS
Retrocopy DHIYRQVVHGKEGSIYLVTGQQVDHSIITAQAGATLNNLMSHAQELVVKLRSLQFDQREFVCLKFLVLFS

Parental  LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPY
          LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPY
Retrocopy LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPY

Parental  NNLLIEMLHAKRA
          NNLLIEMLHAKRA
Retrocopy NNLLIEMLHAKRA

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	0.11 RPM
SRP017611_kidney	0.00 RPM	0.51 RPM
SRP017611_liver	0.85 RPM	12.18 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_811 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_811 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_811 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
Mus musculus	ENSMUSG00000026398	1 retrocopy	retro_mmus_2208,
Oryctolagus cuniculus	ENSOCUG00000006240	1 retrocopy	retro_ocun_811 ,
Otolemur garnettii	ENSOGAG00000025622	1 retrocopy	retro_ogar_2546,