RetrogeneDB ID: retro_pcap_184

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_14230:36552..37291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DNAJA1
• Ensembl ID: ENSPCAG00000012273
• Aliases: None
• Description: DnaJ (Hsp40) homolog, subfamily A, member 1 [Source:HGNC Symbol;Acc:5229]

Sequence

>retro_pcap_184
CACTGCTATTTGCCTGGGGTGCAAATACGAATTCATCAGATAGGACCTGGAATGGTTCACCAAATTCAGTCTGTGTGCAT
GGAGTACCAGGGCCATGGGGAACAGATCAGCCCTAAAGATAGATGTCGAAGTTGCAATGGAAGGAAGATTGTCTGAGAGA
AAATTCTACAAGCTCACATTGACAAAGGAATGAAAGATGGCCAGAAGTTAACACTCCATGGTGAAGGAGACCAAGAGCCA
GTCCTGGAGGTAGGGGATATTATCATTGTTCTAGATCAGAAGGACCATGCTGTTTTTACTAGACTAGGAGAAAACCTCTT
CATGTGGATGGACATACAGCTCGTTGAAACACTGTGTGGCTTCCAGAAGCTGACATCCACTCTTGGTAACTGAACCATAG
TCATACTTCTCATCCAACTCAGATCGTCAAGCATGAAGATATCAAATGTGTGCTATATGAAGGCATGCCAATTTATCATA
GGCCATATGAAAAGGGTACCTAGTCATCCAATTTAAGGTAAACTTCCCTGAGAATGGTTTTCTTTCTCCTGATAAACTTG
TTTTGCTGGAAAAACTCTTACCGGAGAGGAAGGAAGTAAAAGAGACTGGTGAAATGGATCAGGTAGAACTGGTGGACTTT
GATCCAAACCAGGAAAGGCGCTGCCATTGCAACAGAGAAGCATGTTGAGAATGATGACCCAGGCCATCACCCAGAGGGGA
GGTTCAGTACCAGACCTCT

Alignment

ORF - retro_pcap_184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.75 %
• Parental protein coverage: 84.07 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  NCRGTGMQIRIHQIGPGMVQQIQSVCMECQGHGERISPKDRCKSCNGRKIVREKKILEVHIDKGMKDGQK
          .C...G.QIRIHQIGPGMV.QIQSVCME.QGHGE.ISPKDRC.SCNGRKIV.EK.IL..HIDKGMKDGQK
Retrocopy HCYLPGVQIRIHQIGPGMVHQIQSVCMEYQGHGEQISPKDRCRSCNGRKIV*EK-ILQAHIDKGMKDGQK

Parental  ITFHGEGDQEPGLEPGDIIIVLDQKDHAVFTRRGEDLFMCMDIQLVEALCGFQKPISTLDNRTIVI-TSH
          .T.HGEGDQEP.LE.GDIIIVLDQKDHAVFTR.GE.LFM.MDIQLVE.LCGFQK..STL.N.TIVI.TSH
Retrocopy LTLHGEGDQEPVLEVGDIIIVLDQKDHAVFTRLGENLFMWMDIQLVETLCGFQKLTSTLGN*TIVI<TSH

Parental  PGQIVKHEDIKCVLNEGMPIYRRPYEKGR-LIIQFKVNFPENGFLSPDKLALLEKLLPERKEVEETDEMD
          P.QIVKHEDIKCVL.EGMPIY.RPYEKG..L.IQFKVNFPENGFLSPDKL.LLEKLLPERKEV.ET.EMD
Retrocopy PTQIVKHEDIKCVLYEGMPIYHRPYEKGT<LVIQFKVNFPENGFLSPDKLVLLEKLLPERKEVKETGEMD

Parental  QVELVDFDPNQERRRHYNGEA-YEDDDTDHH-PRGGVQCQTS
          QVELVDFDPNQERR.H.N.EA..E.DD..HH.PRG.VQ.QTS
Retrocopy QVELVDFDPNQERRCHCNREA>VENDDPGHH<PRGEVQYQTS

Legend:

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

Expression

RNA-Seq

Procavia capensis was not studied using RNA-Seq expression data.

ChIP-Seq

Procavia capensis was not studied using ChIP-Seq data.

EST

Procavia capensis was not studied using EST data.

TSS

Procavia capensis was not studied using FANTOM5 data.

Lab

retro_pcap_184 was not experimentally validated.

Homology

Retrocopy orthology:

Procavia capensis 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 15 parental genes, and 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007589	4 retrocopies	retro_amel_1509, retro_amel_455, retro_amel_756, retro_amel_946,
Canis familiaris	ENSCAFG00000001818	23 retrocopies	retro_cfam_1111, retro_cfam_1153, retro_cfam_1218, retro_cfam_1229, retro_cfam_1315, retro_cfam_1352, retro_cfam_1420, retro_cfam_1457, retro_cfam_1520, retro_cfam_1668, retro_cfam_1833, retro_cfam_1941, retro_cfam_1949, retro_cfam_1994, retro_cfam_2004, retro_cfam_2162, retro_cfam_352, retro_cfam_391, retro_cfam_419, retro_cfam_749, retro_cfam_751, retro_cfam_923, retro_cfam_993,
Callithrix jacchus	ENSCJAG00000008022	10 retrocopies	retro_cjac_1645, retro_cjac_1777, retro_cjac_2015, retro_cjac_2120, retro_cjac_2730, retro_cjac_2731, retro_cjac_2763, retro_cjac_3037, retro_cjac_3762, retro_cjac_887,
Cavia porcellus	ENSCPOG00000000462	6 retrocopies	retro_cpor_1456, retro_cpor_225, retro_cpor_386, retro_cpor_396, retro_cpor_561, retro_cpor_781,
Gorilla gorilla	ENSGGOG00000007030	3 retrocopies	retro_ggor_1603, retro_ggor_2463, retro_ggor_418,
Myotis lucifugus	ENSMLUG00000016086	7 retrocopies	retro_mluc_1245, retro_mluc_1485, retro_mluc_1737, retro_mluc_1878, retro_mluc_2062, retro_mluc_2579, retro_mluc_576,
Monodelphis domestica	ENSMODG00000003384	7 retrocopies	retro_mdom_1140, retro_mdom_1253, retro_mdom_1451, retro_mdom_1627, retro_mdom_1824, retro_mdom_742, retro_mdom_874,
Mus musculus	ENSMUSG00000028410	3 retrocopies	retro_mmus_2561, retro_mmus_2982, retro_mmus_3507,
Procavia capensis	ENSPCAG00000012273	2 retrocopies	retro_pcap_184 , retro_pcap_220,
Pteropus vampyrus	ENSPVAG00000011470	1 retrocopy	retro_pvam_672,
Rattus norvegicus	ENSRNOG00000007029	2 retrocopies	retro_rnor_2208, retro_rnor_608,
Sorex araneus	ENSSARG00000001373	5 retrocopies	retro_sara_280, retro_sara_312, retro_sara_671, retro_sara_741, retro_sara_748,
Sarcophilus harrisii	ENSSHAG00000012366	1 retrocopy	retro_shar_762,
Ictidomys tridecemlineatus	ENSSTOG00000005200	4 retrocopies	retro_itri_265, retro_itri_303, retro_itri_378, retro_itri_809,
Tarsius syrichta	ENSTSYG00000001329	4 retrocopies	retro_tsyr_110, retro_tsyr_1384, retro_tsyr_1921, retro_tsyr_57,