RetrogeneDB ID: retro_opri_731

Retrocopy location

• Organism: Southern American pika (Ochotona princeps)
• Coordinates: scaffold_2671:142689..143630(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SMARCE1
• Ensembl ID: ENSOPRG00000000985
• Aliases: None
• Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 [Source:HGNC Symbol;Acc:11109]

Sequence

>retro_opri_731
ATGTCAAAAATTCTATCTTATGCCTCACCTCCCACCCCAGTTCCTGCAACACAAATGTGCAGCACACCAGGGCTTGTGGA
ATACAATCTGTACAGTCATGTTGCCTACAACAACTATGGGGTTGGAGGAAACCCAAGCACCAACAGCCAGGGCTTGCTGC
CTCTGGTGTTATGATTCCCAAACTCCTCAAACCACCAGATAAGCCACTGATGCCCTATATGAGGTGCAGAAGAAAGGTCT
GTGATGAAATAAATGCTTCCAACCCTAACCTATAGTTGTGGGAGATTGGAAAGATTTTGGTGGCATGTAGTGAGAGTTCA
TCGATGAAGAGGAACAAGAGTATTTAAACAAACAAAAAGCAGAGAAAATCAAGTACATTGAATCCATGAAGGTGTATCAC
AATTCCCATGGCATACCTGACTGGCGTCAATGCCAAAGTCATGCAGAGGCCGTCCTGGAGAAGCTGACAGAGAGTCTAGC
ATGGAGAAAGGGGAGTCATACAGGAGCGTCTATCTCCCAGAAGACCCTGATGATTATGATGATGGCTTTTCAATGAAGCA
TACGCTATCGCTGGTTTCCACAGAAACCACTGCCTCATTAGTGAGATTCTCAGTGAGACTGTGGTGCTCCACATGCAGTC
TGTCGTCACAACAGCTTTAATGCAGGTCCTTAAGCAATGTGTCCAGTCTTTAATGGTTCATCAGCAACAGGTGGAAACTT
AACTTCTTCAAATAGAGGAGTGACACCAGCAAAAGCAAAGGAAATGCCTTAGAAAGCACAGATTCATTTAACAATGAACT
CAAAAGATTGTGCTGCTTGAAGGTAGAGACAAATACGGAAAAGTTGCATCTGAAGTTACACAGGCAGAACAGCAGGCCCG
CATAGGGCAGGAGGAGAGGGAGAAGGAAGTAGCAGGGCAGGCCAAGTGCATCCAGATAAGT

Alignment

ORF - retro_opri_731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.69 %
• Parental protein coverage: 77.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MSKRPSYAPPPTPAPATQMPSTPGFVGYNPYSHLAYNNYRLGGNPGTNSR-VTASSGITIPKPPKPPDKP
          MSK..SYA.PPTP.PATQM.STPG.V.YN.YSH.AYNNY..GGNP.TNS....A.SG..IPK..KPPDKP
Retrocopy MSKILSYASPPTPVPATQMCSTPGLVEYNLYSHVAYNNYGVGGNPSTNSQ<GLAASGVMIPKLLKPPDKP

Parental  LMPYMRYSRKVWDQVKASNPDLKLWEIGKII-GGMWRDLTDEEKQEYLNEYEAEKIEYNESMKAYHNS-P
          LMPYMR..RKV.D...ASNP.L.LWEIGKI..GGM.....DEE.QEYLN...AEKI.Y.ESMK.YHNS..
Retrocopy LMPYMRCRRKVCDEINASNPNL*LWEIGKIL<GGM**EFIDEEEQEYLNKQKAEKIKYIESMKVYHNS>M

Parental  AYLAYINAK-SRAEAALE-EESRQRQSRMEKGEPYMSIQPAEDPDDYDDGFSMKHT-ATARFQRNHRLIS
          AYL...NAK.S.AEA.LE.E..R...S.MEKGE.Y.S....EDPDDYDDGFSMKHT.A.A.F.RNH.LIS
Retrocopy AYLTGVNAK<SHAEAVLE<EADRE--SSMEKGESYRSVYLPEDPDDYDDGFSMKHT<AIAGFHRNHCLIS

Parental  EILSESVVPDVRSVVTTARMQVLKRQVQSLMVHQRKLEAELLQIEERHQEKKRK-FLESTDSFNNELKRL
          EILSE.VV....SVVTTA.MQVLK..VQSLMVHQ...E..LLQIEE.HQ.K.RK..LESTDSFNNELKRL
Retrocopy EILSETVVLHMQSVVTTALMQVLKQCVQSLMVHQQQVET*LLQIEE*HQQKQRK>ALESTDSFNNELKRL

Parental  CGLKVEVDME-KIAAEIAQAEEQARKRQEEREKEAAEQAERTQSS
          C.LKVE...E.K.A.E..QAE.QAR..QEEREKE.A.QA...Q.S
Retrocopy CCLKVETNTE<KVASEVTQAEQQARIGQEEREKEVAGQAKCIQIS

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_731 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 17 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013573	4 retrocopies	retro_cjac_1107, retro_cjac_2109, retro_cjac_50, retro_cjac_854,
Homo sapiens	ENSG00000073584	5 retrocopies	retro_hsap_1195, retro_hsap_1304, retro_hsap_3623, retro_hsap_3947, retro_hsap_922,
Gorilla gorilla	ENSGGOG00000011803	2 retrocopies	retro_ggor_1020, retro_ggor_931,
Microcebus murinus	ENSMICG00000009821	4 retrocopies	retro_mmur_1408, retro_mmur_1592, retro_mmur_608, retro_mmur_928,
Myotis lucifugus	ENSMLUG00000004609	1 retrocopy	retro_mluc_1209,
Macaca mulatta	ENSMMUG00000004005	3 retrocopies	retro_mmul_1284, retro_mmul_2159, retro_mmul_2286,
Mustela putorius furo	ENSMPUG00000014660	4 retrocopies	retro_mputfur_1411, retro_mputfur_1482, retro_mputfur_1499, retro_mputfur_739,
Mus musculus	ENSMUSG00000037935	5 retrocopies	retro_mmus_1111, retro_mmus_1127, retro_mmus_2437, retro_mmus_2618, retro_mmus_3194,
Nomascus leucogenys	ENSNLEG00000001957	4 retrocopies	retro_nleu_1060, retro_nleu_2051, retro_nleu_2083, retro_nleu_286,
Oryctolagus cuniculus	ENSOCUG00000008981	1 retrocopy	retro_ocun_59,
Otolemur garnettii	ENSOGAG00000001652	7 retrocopies	retro_ogar_1734, retro_ogar_2059, retro_ogar_3199, retro_ogar_402, retro_ogar_454, retro_ogar_682, retro_ogar_760,
Ochotona princeps	ENSOPRG00000000985	1 retrocopy	retro_opri_731 ,
Pongo abelii	ENSPPYG00000008456	4 retrocopies	retro_pabe_2973, retro_pabe_3251, retro_pabe_794, retro_pabe_994,
Pan troglodytes	ENSPTRG00000022902	5 retrocopies	retro_ptro_2451, retro_ptro_2678, retro_ptro_3039, retro_ptro_639, retro_ptro_894,
Pteropus vampyrus	ENSPVAG00000011355	1 retrocopy	retro_pvam_237,
Rattus norvegicus	ENSRNOG00000010676	7 retrocopies	retro_rnor_1278, retro_rnor_1311, retro_rnor_1456, retro_rnor_1507, retro_rnor_1599, retro_rnor_2383, retro_rnor_2593,
Tupaia belangeri	ENSTBEG00000000770	10 retrocopies	retro_tbel_1246, retro_tbel_1554, retro_tbel_2208, retro_tbel_2955, retro_tbel_4035, retro_tbel_4629, retro_tbel_4656, retro_tbel_658, retro_tbel_821, retro_tbel_844,