RetrogeneDB ID: retro_ocun_777

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 14:125346387..125347807(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSOCUG00000013417
• Aliases: None
• Description: None

Sequence

>retro_ocun_777
CAGGTTACTCACTATAAACAATACCCACCCAACACAAGCAAAGTTTATTCCTACTTTGAATGCCGTGAAAAGAAGACAGA
AAACTCCAAAGTAAGGAAGGTGAAATACGAGGAAACAGTATTTTATGGGTTGCAGTACATTCTTAATAAGTACTTAAAAG
GCAAAGTAGTGACCAAAGAGAAAATCCAGGAAGCCAAAGAGGTCTACAGAGAACATTTCCAAGATGATGTCTTTAATGAA
AAGGGATGGAACTACATTCTGGAGAAATACGACGGGCATCTTCCAATAGAAGTCAAGGCTGTTCCTGAGGGCTCCGTGGT
TCCCAAAGGAAACGTCCTCTTCACAGTGGAGAACACAGACCCCGAGTGCTACTGGCTCACAAACTGGATTGAGACTATTC
TTGTTCAGTCCTGGTATCCAATCACAGTGGCTACAAATTCTAGAGAGCAGAAGAAAATATTGGCCAAATATTTGCTAGAA
ACTTCCGGTAACTTAGATGGTCTGGAATACAAGTTACATGATTTTGGCTACAGAGGAGTCTCTTCTCAAGAGACTGCTGG
CATAGGAGCATCTGCTCATTTGGTTAACTTCAAAGGAACAGATACAGTAGCAGGAATTGCTCTGATTAAAAAATACTACG
GGACAAAAGATCCCATTCTGGGCTATTCTCTGCCAGCAGCGGAACACAGTACCATAACAGCTTGAGGGAAAGACCATGAA
AAAGATGCATTTGAACATATAGTAACACAGTTTTCCTCAGTGCCTGTATCTGTGGTCAGCGACAGCTATGACATCTATAA
TGCGTGTGAGAAAATATGGGGAGAAGACCTAAGACATTTAATAGTATCAAGAAGTACAGAGGCACCACTAATAATCAGAC
CTGATTCTGGAAATCCTCTTGACACTGTATTAAAGGTTTTGGATATTTTAGGTAAGAAATTTCCTGTTGTTGAGAATTCG
AAAGGCTACAAGTTGCTGCCACCGTATCTTAGAGTTATTCAAGGGGATGGAGTGGATATTAATACCTTACAAGAGATTGT
AGAAGGCATGAAACAAAAAAAAGTGGAGTATTGAAAATATTGCCTTCGGCTCTGGTGGAGCTTTGCTACAGAAGTTGACA
AGAGACCTCTTGAATTGTTCCTTCAAGTGTAGTTACGTTGTAACCAACGGTCTCGGGATTAATGTCTTCAAGGACCCGGT
CGCTGATCCCAACAAAAGGTCCAAAAAGGGCCGCTTATCTTTGCATAGGACACCAGCGGGGAATTTTGTTACACTGGAAG
AAGGAAAGGGAGACCTTGAAGAATACGGTCATGATCTTCTCCATACTGTCTTCAAGAATGGTAAGGTGACAAAAAGCTAT
TCCTTTGATGAAGTAAGGAAAAACGCACGGCTGAATATTGAACTGGAAGCAGATCCTCAT

Alignment

ORF - retro_ocun_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.95 %
• Parental protein coverage: 96.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KVTHYKQYPPNTSKVYSYFECREKKTENSKVRKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKEVYR
          .VTHYKQYPPNTSKVYSYFECREKKTENSKVRKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKEVYR
Retrocopy QVTHYKQYPPNTSKVYSYFECREKKTENSKVRKVKYEETVFYGLQYILNKYLKGKVVTKEKIQEAKEVYR

Parental  EHFQDDVFNEKGWNYILEKYDGHLPIEVKAVPEGSVVPRGNVLFTVENTDPECYWLTNWIETILVQSWYP
          EHFQDDVFNEKGWNYILEKYDGHLPIEVKAVPEGSVVP.GNVLFTVENTDPECYWLTNWIETILVQSWYP
Retrocopy EHFQDDVFNEKGWNYILEKYDGHLPIEVKAVPEGSVVPKGNVLFTVENTDPECYWLTNWIETILVQSWYP

Parental  ITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGIALIK
          ITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGIALIK
Retrocopy ITVATNSREQKKILAKYLLETSGNLDGLEYKLHDFGYRGVSSQETAGIGASAHLVNFKGTDTVAGIALIK

Parental  KYYGTKDPIPGYSLPAAEHSTITAWGKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHL
          KYYGTKDPI.GYSLPAAEHSTITA.GKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHL
Retrocopy KYYGTKDPILGYSLPAAEHSTITA*GKDHEKDAFEHIVTQFSSVPVSVVSDSYDIYNACEKIWGEDLRHL

Parental  IVSRSTEAPLIIRPDSGNPLDTVLKVLDILGKKFPVVENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGM
          IVSRSTEAPLIIRPDSGNPLDTVLKVLDILGKKFPVVENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGM
Retrocopy IVSRSTEAPLIIRPDSGNPLDTVLKVLDILGKKFPVVENSKGYKLLPPYLRVIQGDGVDINTLQEIVEGM

Parental  KQKK-WSIENIAFGSGGALLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPA
          KQKK.WSIENIAFGSGGALLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPA
Retrocopy KQKK>WSIENIAFGSGGALLQKLTRDLLNCSFKCSYVVTNGLGINVFKDPVADPNKRSKKGRLSLHRTPA

Parental  GNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTKSYSFDEVRKNARLNIELEADPH
          GNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTKSYSFDEVRKNARLNIELEADPH
Retrocopy GNFVTLEEGKGDLEEYGHDLLHTVFKNGKVTKSYSFDEVRKNARLNIELEADPH

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	0.66 RPM	7.12 RPM
SRP017611_kidney	0.41 RPM	11.76 RPM
SRP017611_liver	2.24 RPM	30.91 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_777 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_777 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016193	2 retrocopies	retro_cjac_1281, retro_cjac_3877,
Cavia porcellus	ENSCPOG00000009226	1 retrocopy	retro_cpor_848,
Homo sapiens	ENSG00000105835	1 retrocopy	retro_hsap_79,
Oryctolagus cuniculus	ENSOCUG00000013417	1 retrocopy	retro_ocun_777 ,
Pongo abelii	ENSPPYG00000018270	2 retrocopies	retro_pabe_1407, retro_pabe_1415,
Pan troglodytes	ENSPTRG00000019571	1 retrocopy	retro_ptro_114,
Takifugu rubripes	ENSTRUG00000016695	1 retrocopy	retro_trub_33,