RetrogeneDB ID: retro_opri_186

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_3377:429267..430232(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTSV
• Ensembl ID: ENSOPRG00000001030
• Aliases: None
• Description: cathepsin V [Source:HGNC Symbol;Acc:2538]

Sequence

>retro_opri_186
ATGAATCCTTTATTTCTCCTGGTTGCCCTTTGCTGGGGAATAGCCTTCGCTATTCCAAACTTTGATCAGAATTTAGATAC
ACAATGGTACCAGTGGAAAGCAACACACAAGAGACTCTACGACTTGAATGAAGAAGGATGGAGGAGAGCTGTGTGGGAGA
AGAACAAGATGACTGACCTTCACAATGGGGAATACAGCCAGGCAAGTATGGCTTTACCATGGCCATGAATGTCTATGGCG
GCATGACCAATGAAGAATTCAGACAAGTGATGAATGGCTAACAGCACCAGAAACCCATGCAGGGGAAAATGGTTCATGAA
CCTCTGCTGCTTCAGACCTCCACATCTGTGGATTGACGTGAGAAAGGCTATGTGACTCCCGTGAAGAATCAGGGTCAGTG
TGGTCCCTGTTGGGCATTCAGTGCAACTGACATCCTGGAAGGCCAGATGTTTCAGAAAACTGGCAAACTGGAGTCCCCAA
GTGAGTAGAACCCTGTGGACTGTTCTAAATCCCAGGGCAATATGGGTTGTAATGGTGGCCTCATAGACAACGTCTTTGAA
TATGTGAAAGAGAATGGGGGCCTGGACTCTGAGGAATCCTACCCATATCAAGCTGTTGACGAAATGTGTAAGTACAGGCC
CGAATGCTCTGCAGCCAATGACACGGGCTTCGTGGACATCCTGCAGCATGAGAAGGCTCTCTTGAAAGCTGTGGCCACCG
TGGGGCCCATCTCTGCTGCTATTAATGCAGGATATCCATCCTTCCAGTTCTACAGATCGGGCATTTACTACGACAAAGAA
TGCAGCAGCAAGGAGCTTGATCACAGTGTTCTGGTGGTTGCCTATGGCTTTGAAGGAACACATCCAAACATCACTAAATA
CTGGCTTGTGAAGAACAGCTGGGGTCCAGAATGGAGCATTGATGGCTACGTGAAAATGATCAGAGACAAAGACAACCACT
GAGGT

Alignment

ORF - retro_opri_186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.88 %
• Parental protein coverage: 96.99 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKPLFLLAAVCWGIAFAIPTFDQ-IDTQWYQGKATHXXXXXXNEEGWRRAVWEKNKKMIDLHNGEYSQ-G
          M.PLFLL.A.CWGIAFAIP.FDQ..DTQWYQ.KATH......NEEGWRRAVWEKNK.M.DLHNGEYSQ.G
Retrocopy MNPLFLLVALCWGIAFAIPNFDQNLDTQWYQWKATHKRLYDLNEEGWRRAVWEKNK-MTDLHNGEYSQ<G

Parental  KHGFTMAMNAYGDMTNEEFRQVMNGYQNQRHRQGKMFHEPLLLQTPKSVDWREKGYVTPVKNQGQCGSCW
          K.GFTMAMN.YG.MTNEEFRQVMNG.Q.Q...QGKM.HEPLLLQT..SVD.REKGYVTPVKNQGQCG.CW
Retrocopy KYGFTMAMNVYGGMTNEEFRQVMNG*QHQKPMQGKMVHEPLLLQTSTSVD*REKGYVTPVKNQGQCGPCW

Parental  AFSATGALEGQMFRKTGKLVSLSEQNLVDCSKSQGNMGCNGGLMDNAFEYVKENGGLDSEESYPYEAVDE
          AFSAT..LEGQMF.KTGKL.S.SE.N.VDCSKSQGNMGCNGGL.DN.FEYVKENGGLDSEESYPY.AVDE
Retrocopy AFSATDILEGQMFQKTGKLESPSE*NPVDCSKSQGNMGCNGGLIDNVFEYVKENGGLDSEESYPYQAVDE

Parental  TCKYRPECSAANDTGFVDIQQHEKALLKAVATVGPISAAIDAGHPSFQFYKSGIYYDKECSSKELDHGIL
          .CKYRPECSAANDTGFVDI.QHEKALLKAVATVGPISAAI.AG.PSFQFY.SGIYYDKECSSKELDH..L
Retrocopy MCKYRPECSAANDTGFVDILQHEKALLKAVATVGPISAAINAGYPSFQFYRSGIYYDKECSSKELDHSVL

Parental  VVGYGFEGTHPNITKYWLVKNSWGPEWGIDGYVKMIRDKDNHCG
          VV.YGFEGTHPNITKYWLVKNSWGPEW.IDGYVKMIRDKDNH.G
Retrocopy VVAYGFEGTHPNITKYWLVKNSWGPEWSIDGYVKMIRDKDNH*G

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_186 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 9 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007548	8 retrocopies	retro_chof_1227, retro_chof_1332, retro_chof_1345, retro_chof_141, retro_chof_1464, retro_chof_2392, retro_chof_383, retro_chof_424,
Dasypus novemcinctus	ENSDNOG00000012037	1 retrocopy	retro_dnov_2387,
Macropus eugenii	ENSMEUG00000002168	2 retrocopies	retro_meug_1349, retro_meug_1567,
Macropus eugenii	ENSMEUG00000014293	1 retrocopy	retro_meug_1873,
Macropus eugenii	ENSMEUG00000016209	2 retrocopies	retro_meug_159, retro_meug_1727,
Monodelphis domestica	ENSMODG00000002844	1 retrocopy	retro_mdom_1101,
Ochotona princeps	ENSOPRG00000001030	2 retrocopies	retro_opri_186 , retro_opri_499,
Petromyzon marinus	ENSPMAG00000003453	1 retrocopy	retro_pmar_7,
Tupaia belangeri	ENSTBEG00000016406	1 retrocopy	retro_tbel_2841,