RetrogeneDB ID: retro_ocun_1388

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 7:156782234..156783075(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000023186
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSR1
• Ensembl ID: ENSOCUG00000009083
• Aliases: None
• Description: signal sequence receptor, alpha (SSR1), mRNA [Source:RefSeq mRNA;Acc:NM_001082753]

Sequence

>retro_ocun_1388
ATGAGACTCCTCCCCCACTTGCTCCTGCTTCTGCTGCTCGTGTTCCCGCCACCGTGCTGCTGCAAGGCGGCCCGGGAGGC
TCATTAGCAGAGGCTCAAGATCTTACGGAGGATGAAGAAACAGTGGAAGATTCAGTCATCGAAGACGAAGATGATGAAGC
TGAGGTAGAGAAAGATGAACCCACAGATTTGGCAGAAGATAAGGAAGAAGAAGATGTTTCTGGTGAACCAGAAGCTTCAC
CAAGTGCAGATGCAACTATCTTGTTTGTAAAAGGAGAAGATTTTCCAGCAAATAACATTGTGAAGTTCCTGGTAGGCTTT
ACAAACAAGGGTACAGAAGATTTTATCGTTGAATCCCTAGCTGCCTCTTTTCCTTACCCTCAGGACTACCAGTTTTATAT
ACAGAATTTCACAGCTCTTCCTCTGAACACTATAGTACCACCCCAGAGACAGGCAACTTTCAAGTACTCCTTCATTCCTG
CGGAGCCCATGGGTGGGCGACCCTTTGGTCTGGTCATCAATCTGAACTACAAAGATGTTAACGGTAATGTATTCCAAGAT
GCTGTCTTCAATCAAACAGTTACAGTTATTGAAAGAGAGGATGGGTTAGATGGAGAAACAATCTTTATGTATATGTTCCT
TGCTGGTCTTGGACTTCTGGTTGTTGTTGGACTTCATCAGCTCCTAGAGTCTAGAAAGCGTAAGAGACCTACACAGAAAG
TAGAAATGGGTACATCAAGTCAGAATGATGTTGACATGATTGGATTCCTCAAGAAACTTTGAATCAGATCAATAAAGCTT
CACTGAGATGGCTGCCCAGGAAGAGGGCACAGAAGAGATCG

Alignment

ORF - retro_ocun_1388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.9 %
• Parental protein coverage: 96.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MRLLPRLLLLLLLVFP-ATVLLRGGPGGSLAEAQDLTEDEETVEDSVIEDEDDEAEVEEDEPTDLAEDKE
          MRLLP.LLLLLLLVFP.ATVLL.GGPGGSLAEAQDLTEDEETVEDSVIEDEDDEAEVE.DEPTDLAEDKE
Retrocopy MRLLPHLLLLLLLVFP<ATVLLQGGPGGSLAEAQDLTEDEETVEDSVIEDEDDEAEVEKDEPTDLAEDKE

Parental  EEDVSGEPEASPSADTTILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLDASFRYPQDYQFYIQNFTA
          EEDVSGEPEASPSAD.TILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESL.ASF.YPQDYQFYIQNFTA
Retrocopy EEDVSGEPEASPSADATILFVKGEDFPANNIVKFLVGFTNKGTEDFIVESLAASFPYPQDYQFYIQNFTA

Parental  LPLNTIVPPQRQATFEYSFIPAEPMGGRPFGLVINLNYKDFNGNVFQDAVFNQTVTVIEREDGLDGETIF
          LPLNTIVPPQRQATF.YSFIPAEPMGGRPFGLVINLNYKD.NGNVFQDAVFNQTVTVIEREDGLDGETIF
Retrocopy LPLNTIVPPQRQATFKYSFIPAEPMGGRPFGLVINLNYKDVNGNVFQDAVFNQTVTVIEREDGLDGETIF

Parental  MYMFLAGLGLLVVVGLHQLLESRKRKRPIQKVEMGTSSQNDVDM-SWIPQETLNQISKYSLNKASPRRLP
          MYMFLAGLGLLVVVGLHQLLESRKRKRP.QKVEMGTSSQNDVDM..WIPQETLNQI.K.SL....PR...
Retrocopy MYMFLAGLGLLVVVGLHQLLESRKRKRPTQKVEMGTSSQNDVDM<DWIPQETLNQINKASL-RWLPRKRA

Parental  RKRA
          .KR.
Retrocopy QKRS

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	0.39 RPM	60.65 RPM
SRP017611_kidney	0.41 RPM	63.55 RPM
SRP017611_liver	0.15 RPM	40.39 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1388 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1388 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1388 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000022731	1 retrocopy	retro_btau_1285,
Dasypus novemcinctus	ENSDNOG00000015772	1 retrocopy	retro_dnov_879,
Equus caballus	ENSECAG00000019520	1 retrocopy	retro_ecab_399,
Echinops telfairi	ENSETEG00000020111	1 retrocopy	retro_etel_1983,
Oryctolagus cuniculus	ENSOCUG00000009083	1 retrocopy	retro_ocun_1388 ,
Otolemur garnettii	ENSOGAG00000014234	1 retrocopy	retro_ogar_1465,
Ictidomys tridecemlineatus	ENSSTOG00000022608	1 retrocopy	retro_itri_1850,