RetrogeneDB ID: retro_opri_967

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_511:399677..400356(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAZ
• Ensembl ID: ENSOPRG00000000276
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide [Source:HGNC Symbol;Acc:12855]

Sequence

>retro_opri_967
GACTTGGCAGCCCACATGAAGTCTGTAACCCAGCAAGGAGCTGAGTTATCTAATGAGAGGAGCCTCCTCTCCATTGCCTA
TTAAAAATGTCATAGGAGACTATAGGTCATCATGGAGGGTCGTCTCAAGTGTTGAGCAAAACACCGAAGGTGCTGAGAAA
AAGCAGCAGATGATTCGTGAATACAGGGAGAAAGTTGAGACTGAGCTAAGAGATATTTGCAACGATGTAGTGTGTCTTTT
GGAAAATTTCTTGATCCCCAATGCTTCACAAGCAGCGAACAAGGTCTTCTGTTTGAAAATGAAAGGAGGCTAATGCCGTT
TACCTGGCTGAGGTCACCGCTGGTGACCTGGTGACGACAAGAAGGGGATTGTGGATCAGTCACAACAGGCATACCAAGAT
GCTTTTCAAATCAGCAAAAAGGAGATGCAGCCAACATAGTCCATCAGATCGGGTCTGGCCCTTAACTTCTCTGTGTTCTA
TTACGAGATTCTGAATTCCCCAGGAAAAGCCTGCTCTCTGGCGAAGACGGCTTTCAATGAAGCCCTTGCTGAACTTAATA
CGTTAAGTGAAGAGTCATACAAAGACAGCATGCTAATAATGCAGCTACTGAGAGACAGCTTGACATTGTGAACATCTGAT
ACCCAAGGAGATGAAGCTCGAGCAGAAGAAGGGGAAAAT

Alignment

ORF - retro_opri_967 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.26 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DMAACMKSVTEQGAELSNEERNLLSVAY-KNVVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETE
          D.AA.MKSVT.QGAELSNE.R.LLS.AY.KNV.G..RSSWRVVSS.EQ.TEGAEKKQQM.REYREK.ETE
Retrocopy DLAAHMKSVTQQGAELSNE-RSLLSIAY>KNVIGDYRSSWRVVSSVEQNTEGAEKKQQMIREYREKVETE

Parental  LRDICNDVLSLLEKFLIPNASQAESKVFYLKMKGDYYR-YLAEVAAGD---DKKGIVDQSQQAYQEAFEI
          LRDICNDV..LLE.FLIPNASQA..KVF.LKMKG...R.YLAEV.AGD......G............F..
Retrocopy LRDICNDVVCLLENFLIPNASQAANKVFCLKMKGG*CR>YLAEVTAGDLVTTRRGLWISHNRHTKMLFKS

Parental  SKK-EMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLSEESYKDSTLIMQLLRDL
          .K..EMQPT..IR.GLALNFSVFYYEILNSP.KACSLAKTAF.EA.AEL.TLSEESYKDS.LIMQLLRD.
Retrocopy AKR<EMQPT*SIRSGLALNFSVFYYEILNSPGKACSLAKTAFNEALAELNTLSEESYKDSMLIMQLLRDS

Parental  TXXXXXXXXXXXEAGEGGEN
          ...............E.GEN
Retrocopy LTL*TSDTQGDEARAEEGEN

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_967 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 18 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008694	2 retrocopies	retro_acar_25, retro_acar_44,
Bos taurus	ENSBTAG00000000236	4 retrocopies	retro_btau_1482, retro_btau_635, retro_btau_68, retro_btau_910,
Canis familiaris	ENSCAFG00000000580	6 retrocopies	retro_cfam_1302, retro_cfam_1521, retro_cfam_158, retro_cfam_1840, retro_cfam_233, retro_cfam_465,
Callithrix jacchus	ENSCJAG00000015844	5 retrocopies	retro_cjac_1769, retro_cjac_2164, retro_cjac_3000, retro_cjac_31, retro_cjac_881,
Dasypus novemcinctus	ENSDNOG00000001672	10 retrocopies	retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Ficedula albicollis	ENSFALG00000005860	1 retrocopy	retro_falb_13,
Gallus gallus	ENSGALG00000010725	1 retrocopy	retro_ggal_3,
Gorilla gorilla	ENSGGOG00000022133	9 retrocopies	retro_ggor_1092, retro_ggor_1754, retro_ggor_211, retro_ggor_2379, retro_ggor_2997, retro_ggor_2998, retro_ggor_3020, retro_ggor_499, retro_ggor_544,
Monodelphis domestica	ENSMODG00000006158	8 retrocopies	retro_mdom_1589, retro_mdom_1664, retro_mdom_1763, retro_mdom_1815, retro_mdom_1875, retro_mdom_1958, retro_mdom_255, retro_mdom_446,
Mus musculus	ENSMUSG00000022285	3 retrocopies	retro_mmus_163, retro_mmus_2187, retro_mmus_744,
Oryctolagus cuniculus	ENSOCUG00000000734	2 retrocopies	retro_ocun_1091, retro_ocun_248,
Ochotona princeps	ENSOPRG00000000276	3 retrocopies	retro_opri_1218, retro_opri_218, retro_opri_967 ,
Ochotona princeps	ENSOPRG00000011836	2 retrocopies	retro_opri_56, retro_opri_924,
Pongo abelii	ENSPPYG00000018791	7 retrocopies	retro_pabe_103, retro_pabe_1242, retro_pabe_2047, retro_pabe_3417, retro_pabe_3740, retro_pabe_556, retro_pabe_89,
Pelodiscus sinensis	ENSPSIG00000003703	1 retrocopy	retro_psin_13,
Sarcophilus harrisii	ENSSHAG00000012671	2 retrocopies	retro_shar_126, retro_shar_409,
Sus scrofa	ENSSSCG00000006062	2 retrocopies	retro_sscr_222, retro_sscr_35,
Taeniopygia guttata	ENSTGUG00000012078	1 retrocopy	retro_tgut_4,