RetrogeneDB ID: retro_opri_931

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_4678:131728..132332(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PITPNB
• Ensembl ID: ENSOPRG00000002540
• Aliases: None
• Description: phosphatidylinositol transfer protein, beta [Source:HGNC Symbol;Acc:9002]

Sequence

>retro_opri_931
AAAGTTCCTGCCTTCATGAGGATGATTGCTCCCAAGGATTTCTTGGTGTTTCACAAAAAGTTCTGGAACACCTACCCCTA
CTATAGAACAATTGTAATGTATGAATAGATGAAAGATGATTTCTTCATTAAAATTGAAACATGGCACAAACAAGACTTGG
GAACATTAGAAAATGTACATGGTTTATATCCAAACACATGGAAAATGGTTGAAATTGTCCACATAGATAGTGCAGATCAA
AGTCAAGCTGAACAAGCAGACTACAAAGCTGATGAAGATCAGCATTATTCCAGTCAGTCAAGACCAAGAGAGGCTCTTTG
GGACCCAACTGGAAGAAGGAGCTGGCTAACAAGCCTGACTGTCCCCAGATGTGTGCCTATAAGCTGGTGACCATCAAGTT
CAAGTGGTGGGGACTGCAAAGCAAAGTAGAAAACTTCATTCAGAAGCAAGCAAAAAGGATATTCACAAACTTTCATTGCC
AGCTTTTTTGTTGGATTGACAATTGGATTGATTAGACCATGGAAGACATCAGGAGAATGAAGACGAAACTCAGAAAGAGC
TAGAAACAATGCGTAAAAAGGGTTCCATCCGAGGCACATCAGCT

Alignment

ORF - retro_opri_931 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 74.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KVPAFVRMIAPEGSLVFHEKAWNAYPYCRTIVTNEYMKDDFFIKIETWHKPDLGTLENVHGLDPNTWKTV
          KVPAF.RMIAP...LVFH.K.WN.YPY.RTIV..E.MKDDFFIKIETWHK.DLGTLENVHGL.PNTWK.V
Retrocopy KVPAFMRMIAPKDFLVFHKKFWNTYPYYRTIVMYE*MKDDFFIKIETWHKQDLGTLENVHGLYPNTWKMV

Parental  EIVHIDIADRSQVEPADYKADED-PALFQSVKTKRGPLGPNWKE--LNKPDCPQMCAYKLVTIKFKWWGL
          EIVHID.AD.SQ.E.ADYKADED..ALFQSVKTKRG.LGPNWK....NKPDCPQMCAYKLVTIKFKWWGL
Retrocopy EIVHIDSADQSQAEQADYKADED<SALFQSVKTKRGSLGPNWKKELANKPDCPQMCAYKLVTIKFKWWGL

Parental  QS-VENFIQKQEKRIFTNFHRQLFCWIDKWIDLTMEDIRRM-EDETQKELETLRSQGQVRGTSA
          QS.VENFIQKQ.KRIFTNFH.QLFCWID.WID.TMEDIRRM.EDETQKELET.R..G..RGTSA
Retrocopy QSKVENFIQKQAKRIFTNFHCQLFCWIDNWID*TMEDIRRM<EDETQKELETMRKKGSIRGTSA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ochotona princeps was not studied using RNA-Seq expression data.

ChIP-Seq

Ochotona princeps was not studied using ChIP-Seq data.

EST

Ochotona princeps was not studied using EST data.

TSS

Ochotona princeps was not studied using FANTOM5 data.

Lab

retro_opri_931 was not experimentally validated.

Homology

Retrocopy orthology:

Ochotona princeps does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,