RetrogeneDB ID: retro_ocun_1173

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:106509930..106510884(+)
• Located in intron of: ENSOCUG00000001277

Retrocopy information

• Ensembl ID: ENSOCUG00000023574
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MSN
• Ensembl ID: ENSOCUG00000000149
• Aliases: None
• Description: moesin [Source:HGNC Symbol;Acc:7373]

Sequence

>retro_ocun_1173
ATCAGTGTGCGTGTGACCACCATGGATGCAGAGCTGGAGTTTGCCATCCAGCCCAACACCACTGGCAAGCAGCTGTTTGA
CCAGGTGGTGAAAACGATTGGCCTGAGGGAAGTGTGGTTCTTCGGTCTGCAGTATCAGGACACGAAGGGTTTCTCCACTT
GGCTGAAGCTCAATAAGAAGGTGACTGCCCAGGATGTACGAAAGGAAAGTCCCTTGCTCTTCAAGTTCCGGGCCAAGTTC
TACCCTGAGGATGTATCTGAAGAATTGATCCAGGACATCACCCAGCGCCTATTCTTCCTGCAAGTGAAGGAGGGTATTCT
CATTGATGATATTTACTGCCCTCCTGAGACGGCTGTGCTGCTTGCCTCCTATGCTGTGCAGTCCAAGTATGGTGACTTCA
ATAAGGAGGTGCACAAGGCTGGCTATCTGGCTGGAGACAAGTTGCTGCCACAGAGAGTCCTGGAGCAGCACAAACTCAAC
AAAGACCAGTGGGAGGAGCGAATCCAGGTGTGGCATGAGGAACACCGGGGTATGCTCAGGGAGGATGCAGTCCTGGAATA
TCTGAAGATTGCTCAAGACCTGGAGATGTATGGAGTGAACTACTTCAGCATTAAGAACAAGAAGGGCTCAGAGCTGTGGC
TGGGTGTGGATGCCCTGGGTCTCAACATCTATGAGCAGAATGACAGACTGACTCCCAAGATAGGCTTCCCTTGGAGTGAA
ATCAGAAACATCTCTTTCAACGATAAGAAGTTTGTCATCAAGCCCATTGACAAAAAAGCCCCGGACTTTGTCTTCTATGC
ACCCCGACTGAGGATTAACAAGCGAATCTTGGCCCTGTGCATGGGGAACCATGAGCTATACATGCGCCGCCGCAAGCCTG
ACACCATTGAAGTGCAGCAGATGAAGGCACAGGCCCGGGAGGAGAAGCACCAGAAGCAGATGGAACGTGCTCTA

Alignment

ORF - retro_ocun_1173 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.06 %
• Parental protein coverage: 54.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKES
          ISVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKES
Retrocopy ISVRVTTMDAELEFAIQPNTTGKQLFDQVVKTIGLREVWFFGLQYQDTKGFSTWLKLNKKVTAQDVRKES

Parental  PLLFKFRAKFYPEDVSEELIQDITQRLFFLQVKEGILNDDIYCPPETAVLLASYAVQSKYGDFNKEVHKA
          PLLFKFRAKFYPEDVSEELIQDITQRLFFLQVKEGIL.DDIYCPPETAVLLASYAVQSKYGDFNKEVHKA
Retrocopy PLLFKFRAKFYPEDVSEELIQDITQRLFFLQVKEGILIDDIYCPPETAVLLASYAVQSKYGDFNKEVHKA

Parental  GYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFSIKNKKGS
          GYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFSIKNKKGS
Retrocopy GYLAGDKLLPQRVLEQHKLNKDQWEERIQVWHEEHRGMLREDAVLEYLKIAQDLEMYGVNYFSIKNKKGS

Parental  ELWLGVDALGLNIYEQNDRLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRILALC
          ELWLGVDALGLNIYEQNDRLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRILALC
Retrocopy ELWLGVDALGLNIYEQNDRLTPKIGFPWSEIRNISFNDKKFVIKPIDKKAPDFVFYAPRLRINKRILALC

Parental  MGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQMERCM
          MGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQMER..
Retrocopy MGNHELYMRRRKPDTIEVQQMKAQAREEKHQKQMERAL

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	3.20 RPM	10.60 RPM
SRP017611_kidney	32.33 RPM	92.94 RPM
SRP017611_liver	2.47 RPM	8.02 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1173 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1173 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1173 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147065	1 retrocopy	retro_hsap_3153,
Gorilla gorilla	ENSGGOG00000001823	1 retrocopy	retro_ggor_1359,
Macropus eugenii	ENSMEUG00000015240	1 retrocopy	retro_meug_1267,
Oryctolagus cuniculus	ENSOCUG00000000149	1 retrocopy	retro_ocun_1173 ,
Pongo abelii	ENSPPYG00000020419	1 retrocopy	retro_pabe_2623,
Tursiops truncatus	ENSTTRG00000002946	1 retrocopy	retro_ttru_173,