RetrogeneDB ID: retro_opri_4

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: GeneScaffold_4014:134632..135832(+)
• Located in intron of: ENSOPRG00000009538

Retrocopy information

• Ensembl ID: ENSOPRG00000009559
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: DDI2
• Ensembl ID: ENSOPRG00000018448
• Aliases: None
• Description: DNA-damage inducible 1 homolog 2 (S. cerevisiae) [Source:HGNC Symbol;Acc:24578]

Sequence

>retro_opri_4
ATGCTGCTCACTGTGTACTGTGTACGGAGGGACCTAACAGAGGTAACCTTCTCCCTCCAGGTCAGTCCTGACTTTGAGCT
CCATGACTTCCGAGTCCTTTGTGAGACAGAGTCCAGAATCCCTGCTGAGGAGATGCAGATCATTTACATGGAGAGACTCC
TGGCTGATGACCACTGCTCCTTGGGCTCCTATGGCCTCAAAGACGGTGATGTCATCGTACTACTTCAGAAGGAAAATGTG
GGACCCTGGCCTCCAGGACGTACTCTGAATCAGCCTCGAACGGACTTCAATGGAATTGCAGTGCCTGGGACATCGAACTC
TCGGTGGCAGCAGCCACCGCCATGGGTACCTTCTGCTCATCAGTCCCATGGCTTGGCCTCTGGAGAGAAGATGGTATCTG
CTCAAGATCTGAACAACCCTGCCTTAGTCCGTAGCATGTTACTGTCCAATCCCCACGATCTGTCTCTGCTGAAGGAACGC
AACCCTTCCTTGGCAGAAGCTCTGCTCAGCGGGAATCTTGAAACATTTTCTCAGGTCTTGATGGAGCAGCAGAGGGAAAG
GGCCCTGAGAGAGCAAGAGAGGCTTCGCCTCTACACTGCTGACCCATTTGATAGGGAAGCTCAAGCCAGAATAGAAGAAG
AGATCCGGCAGCAGAACATAGAAGAAAACATGAGTATAGCAATGGAGGAGGCCCCCGAGAGTTTTGGACAAGTGGCCATG
CTCTACATAAACTGCAAAGTGAATGGACATCCTTTGAAGGCTTTTGTTGACTCCGGCGCCCAGATGACCATTATGAGCCA
AGCTTGCGCAGAGAGATGTAACATAATAAGACTAGTAGATCGACGGTGGGCTGGAGTGGCAAAAGGAGTGGGCACACAAA
GAATTATCGGCCGTGTTCATTTAGCTCAGATTCAAATCGAAGGAGACTTCTTGCCATGCTCTTTCTCTATTCTGGAGGAA
CAGCCCATGGATATGCTTCTTGGACTCGACATGCTCAAGAGGCATCAGTGTTCCATTGATTTAAAGAAAAATGTGCTGGT
GATTGGCACCACTGGCACACAGACGCCCTTTCTTCCTGAGGGAGAGTTACCCCCTTGCGCTAAGCTGGTAAGTGATACTG
GGCAAGAAGAGTCTACAGACAAGAAGGCAGCAAACACCTTTAAGCATTCATTCAAGGATTCAGGACGGAAAAAGCATTGA

Alignment

ORF - retro_opri_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.08 %
• Parental protein coverage: 83.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLTVYCVRRDLSEVTFSLQVDADFELHNFRALCKLESGIPAAESQIVYAERPLTDNHRSLASYGLKDGD
          MLLTVYCVRRDL.EVTFSLQV..DFELH.FR.LC..ES.IPA.E.QI.Y.ER.L.D.H.SL.SYGLKDGD
Retrocopy MLLTVYCVRRDLTEVTFSLQVSPDFELHDFRVLCETESRIPAEEMQIIYMERLLADDHCSLGSYGLKDGD

Parental  VVILRQKENTDPRPPVQFPNLPRIDFSSIAVPGTSSSR-QRQPAAVKPSHPS----PGETSASPQGLDNP
          V..L.QKEN..P.PP....N.PR.DF..IAVPGTS.SR.Q..P..V...H.S.....GE...S.Q.L.NP
Retrocopy VIVLLQKENVGPWPPGRTLNQPRTDFNGIAVPGTSNSRWQQPPPWVPSAHQSHGLASGEKMVSAQDLNNP

Parental  ALLRDMLLANPHELSLLKERNPPLAEALLSGDLERFSRVLVEQQQDRARREQERIRLFSADPFDLEAQAK
          AL.R.MLL.NPH.LSLLKERNP.LAEALLSG.LE.FS.VL.EQQ..RA.REQER.RL..ADPFD.EAQA.
Retrocopy ALVRSMLLSNPHDLSLLKERNPSLAEALLSGNLETFSQVLMEQQRERALREQERLRLYTADPFDREAQAR

Parental  IEEDIRQQNIEENMTIAMEEAPESFGQVVMLYINCKVNGHPVKAFVDSGAQMTIMSQACAERCNIMRLVD
          IEE.IRQQNIEENM.IAMEEAPESFGQV.MLYINCKVNGHP.KAFVDSGAQMTIMSQACAERCNI.RLVD
Retrocopy IEEEIRQQNIEENMSIAMEEAPESFGQVAMLYINCKVNGHPLKAFVDSGAQMTIMSQACAERCNIIRLVD

Parental  RRWAGIAKGVGTQKIIGRVHLAQVQIEGDFLACSCSI
          RRWAG.AKGVGTQ.IIGRVHLAQ.QIEGDFL.CS.SI
Retrocopy RRWAGVAKGVGTQRIIGRVHLAQIQIEGDFLPCSFSI

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_4 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 24 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011873	1 retrocopy	retro_amel_10,
Bos taurus	ENSBTAG00000018718	2 retrocopies	retro_btau_15, retro_btau_650,
Canis familiaris	ENSCAFG00000016220	1 retrocopy	retro_cfam_193,
Callithrix jacchus	ENSCJAG00000008625	1 retrocopy	retro_cjac_196,
Cavia porcellus	ENSCPOG00000020885	1 retrocopy	retro_cpor_88,
Equus caballus	ENSECAG00000000762	1 retrocopy	retro_ecab_110,
Homo sapiens	ENSG00000197312	1 retrocopy	retro_hsap_96,
Gorilla gorilla	ENSGGOG00000013537	1 retrocopy	retro_ggor_143,
Macropus eugenii	ENSMEUG00000006148	1 retrocopy	retro_meug_1364,
Myotis lucifugus	ENSMLUG00000030669	1 retrocopy	retro_mluc_68,
Macaca mulatta	ENSMMUG00000019912	1 retrocopy	retro_mmul_231,
Monodelphis domestica	ENSMODG00000003515	1 retrocopy	retro_mdom_282,
Mustela putorius furo	ENSMPUG00000016332	1 retrocopy	retro_mputfur_1509,
Mus musculus	ENSMUSG00000078515	1 retrocopy	retro_mmus_67,
Oryctolagus cuniculus	ENSOCUG00000023891	1 retrocopy	retro_ocun_249,
Otolemur garnettii	ENSOGAG00000027709	1 retrocopy	retro_ogar_4,
Ochotona princeps	ENSOPRG00000018448	1 retrocopy	retro_opri_4 ,
Pongo abelii	ENSPPYG00000001841	1 retrocopy	retro_pabe_158,
Pan troglodytes	ENSPTRG00000024059	1 retrocopy	retro_ptro_570,
Pteropus vampyrus	ENSPVAG00000005084	1 retrocopy	retro_pvam_420,
Rattus norvegicus	ENSRNOG00000012274	1 retrocopy	retro_rnor_2606,
Sus scrofa	ENSSSCG00000003462	1 retrocopy	retro_sscr_6,
Ictidomys tridecemlineatus	ENSSTOG00000019447	1 retrocopy	retro_itri_93,
Tarsius syrichta	ENSTSYG00000002522	1 retrocopy	retro_tsyr_1120,