RetrogeneDB ID: retro_ocun_1620

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018719:1513886..1514695(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PITPNB
• Ensembl ID: ENSOCUG00000000511
• Aliases: None
• Description: phosphatidylinositol transfer protein, beta [Source:HGNC Symbol;Acc:9002]

Sequence

>retro_ocun_1620
GTGCTCATTAAGGAATTCCGGGTGGGCTTGCCATGTTCAGTCCAGGAGTATCAGGTTGGACAGCTTTACTCTGTTGCAGA
AGCTAGTAAGAATGAGACTGGTGGTGGAGAAGGAATTGAAGTCTTAAAGAATGAACTGTATGAGGAAGATGGAGAAAAGA
GACAACATACACATAAAATTTACCATCTGAAGAGCAAAGTTCCTGCTTTCGTGAGGATGATTGCTCCCGAGGGTTCCTTG
GTGTTTCATGAAAAAGCCTGGAACAGCTACCCCTGCTGTAGAACAATTGCAACAATGAATATATGAAAGATGATTTCGTC
ATTAAAATTGAAACATGACACAAACCAGACTTGGGAACATTAGAAAACGTACATGGTTTAGATCCAAACACGTGGAAAAC
AGTCGAAATTGTCCACATAGATATTGCAGATCGAAATCAAGTTGAACCAGCAGACTACAAAGCTGATGAAGATCCAGCAT
TAGTCCAGTCAGTCAAGACCAAGAGAGGCCCTTTGGGACCCAACTGGAAGAAGGAGCTGGCAAACAAGCCTGACTGTCCT
CAGATGTGAGCCTATAAGCTGGTGACCATCAAGTTCAAGTGGTGGGGGATGCAAAGCAAAGCAGAGAACTTCATTCAGAA
ACAAGAAAAAAGGATATTTACAAACTTTCATCGCCAGCTTTTTTGTTGGATTGACAAGTGGATTGATCTGACAATGGAAG
ACATTAGGAGAACGGAAGATGAAACTCAAAAAGAACTAGAAACAATGGGTAAGAAGGGTTCCGTCTGAGGCACGTCAGCT
GCTGATGTC

Alignment

ORF - retro_ocun_1620 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.14 %
• Parental protein coverage: 99.63 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MIIEISRVVLPCSVQEYQVGQLYSVAEASKNETGGGEGIEVLKNEPYEKDGEKGQYTHKIYHLKSKVPAF
          ..I...RV.LPCSVQEYQVGQLYSVAEASKNETGGGEGIEVLKNE.YE.DGEK.Q.THKIYHLKSKVPAF
Retrocopy VLIKEFRVGLPCSVQEYQVGQLYSVAEASKNETGGGEGIEVLKNELYEEDGEKRQHTHKIYHLKSKVPAF

Parental  VRMIAPEGSLVFHEKAWNAYPYCRTIVT-NEYMKDDFFIKIETWHKPDLGTLENVHGLDPNTWKTVEIVH
          VRMIAPEGSLVFHEKAWN.YP.CRTI.T.NEYMKDDF.IKIET.HKPDLGTLENVHGLDPNTWKTVEIVH
Retrocopy VRMIAPEGSLVFHEKAWNSYPCCRTIAT<NEYMKDDFVIKIET*HKPDLGTLENVHGLDPNTWKTVEIVH

Parental  IDIADRSQVEPADYKADEDPALFQSVKTKRGPLGPNWKKELANKPDCPQMCAYKLVTIKFKWWGLQSKVE
          IDIADR.QVEPADYKADEDPAL.QSVKTKRGPLGPNWKKELANKPDCPQM.AYKLVTIKFKWWG.QSK.E
Retrocopy IDIADRNQVEPADYKADEDPALVQSVKTKRGPLGPNWKKELANKPDCPQM*AYKLVTIKFKWWGMQSKAE

Parental  NFIQKQEKRIFTNFHRQLFCWIDKWIDLTMEDIRRMEDETQKELETMRKKGSVRGTSAADV
          NFIQKQEKRIFTNFHRQLFCWIDKWIDLTMEDIRR.EDETQKELETM.KKGSV.GTSAADV
Retrocopy NFIQKQEKRIFTNFHRQLFCWIDKWIDLTMEDIRRTEDETQKELETMGKKGSV*GTSAADV

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	2.76 RPM	94.54 RPM
SRP017611_kidney	1.42 RPM	59.90 RPM
SRP017611_liver	2.08 RPM	90.56 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1620 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1620 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1620 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012309	2 retrocopies	retro_chof_2374, retro_chof_860,
Cavia porcellus	ENSCPOG00000012298	1 retrocopy	retro_cpor_957,
Macropus eugenii	ENSMEUG00000010442	3 retrocopies	retro_meug_392, retro_meug_689, retro_meug_786,
Oryctolagus cuniculus	ENSOCUG00000000511	1 retrocopy	retro_ocun_1620 ,
Otolemur garnettii	ENSOGAG00000000391	1 retrocopy	retro_ogar_1300,
Ochotona princeps	ENSOPRG00000002540	1 retrocopy	retro_opri_931,
Tupaia belangeri	ENSTBEG00000000293	1 retrocopy	retro_tbel_4285,
Takifugu rubripes	ENSTRUG00000018546	1 retrocopy	retro_trub_36,
Tarsius syrichta	ENSTSYG00000001148	1 retrocopy	retro_tsyr_503,
Tursiops truncatus	ENSTTRG00000001278	2 retrocopies	retro_ttru_1060, retro_ttru_1439,