RetrogeneDB ID: retro_pcap_328

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_38417:7668..8205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB3
• Ensembl ID: ENSPCAG00000001945
• Aliases: None
• Description: high mobility group box 3 [Source:HGNC Symbol;Acc:5004]

Sequence

>retro_pcap_328
ATGGATAAAAATGACCCAAAGAAACCAAAGGGCAAGACAACTGCTTATCTGTTGTTAGCACAGACATACAGAGAGGAACA
CAAAAAGAAAAACCCAGAGATTCCTGTCAAATTTTCCAAAAAGTGTTCTGAGAAGTGTTACAACAATGTCTGGGAAAGAG
AAATTCAAATATGATGAATCAAAAAGGGGGACAAAATATGCTATGATCCAGAAATAAAGGATTATGGGCCACCAAGAGAA
ACAAGAAGATCAATCCTAATTCCCTCAAACAAGCAGTCTGGATTCTTATCGCTCTGTTCAGAATTCTGTTCCAAGATTGA
ATCTACAAACTCTGGCATCTCTATCAGACACGTGTCTCAAAAGATGGATGAGATGTGGAATAACTTGGGTGACACTGAGA
AACAGCCTTACAACAAAGTACCAAAACTGAAGAAGTACAAGAAGGGTGTTGCCAACTCTAAGTCTAAAGAGAAGTTTGAT
GGCACAAAGGATCCTGTTAAAGTTGCATACAGAAAGGTAAAAGAAAAGGAACAAAAA

Alignment

ORF - retro_pcap_328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.68 %
• Parental protein coverage: 92.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMFW-KEKSKFDE-MAKPDK
          M.K.DPKKPKGK..AY....QT.REEHKKKNPE.PV....FSKKCSE......W.KEK.K.DE...K.DK
Retrocopy MDKNDPKKPKGKTTAYLLLAQTYREEHKKKNPEIPV---KFSKKCSEKCYNNVW>KEKFKYDE<IKKGDK

Parental  VRYDREMKDYGPAKGKKKKDPNAPKRPPSGFFLFCSDFRPKVKSTNPGISIGDVAKKLGEMWNNLSDSEK
          ..YD.E.KDYGP...........P....SGF...CS.F..K..STN.GISI..V..K..EMWNNL.D.EK
Retrocopy ICYDPEIKDYGPPR-ETRRSILIPSNKQSGFLSLCSEFCSKIESTNSGISIRHVSQKMDEMWNNLGDTEK

Parental  QPYNNKAAKLKEKYEKDVADYKSKGKFDGAKGPAKVARKKVEEEEEE
          QPY.NK..KLK.KY.K.VA..KSK.KFDG.K.P.KVA..KV.E.E..
Retrocopy QPY-NKVPKLK-KYKKGVANSKSKEKFDGTKDPVKVAYRKVKEKEQK

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_328 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 25 parental genes, and 128 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005150	2 retrocopies	retro_btau_190, retro_btau_38,
Canis familiaris	ENSCAFG00000028715	1 retrocopy	retro_cfam_1537,
Choloepus hoffmanni	ENSCHOG00000005005	2 retrocopies	retro_chof_1891, retro_chof_2010,
Callithrix jacchus	ENSCJAG00000003936	9 retrocopies	retro_cjac_1596, retro_cjac_1950, retro_cjac_2343, retro_cjac_2469, retro_cjac_2470, retro_cjac_2738, retro_cjac_2900, retro_cjac_688, retro_cjac_965,
Equus caballus	ENSECAG00000020596	1 retrocopy	retro_ecab_890,
Echinops telfairi	ENSETEG00000015689	4 retrocopies	retro_etel_104, retro_etel_1272, retro_etel_385, retro_etel_465,
Felis catus	ENSFCAG00000024624	4 retrocopies	retro_fcat_1480, retro_fcat_1504, retro_fcat_265, retro_fcat_865,
Gorilla gorilla	ENSGGOG00000027164	16 retrocopies	retro_ggor_1371, retro_ggor_1538, retro_ggor_1540, retro_ggor_1651, retro_ggor_1834, retro_ggor_2104, retro_ggor_2250, retro_ggor_2469, retro_ggor_2490, retro_ggor_2580, retro_ggor_272, retro_ggor_2944, retro_ggor_301, retro_ggor_414, retro_ggor_549, retro_ggor_618,
Loxodonta africana	ENSLAFG00000025877	1 retrocopy	retro_lafr_893,
Microcebus murinus	ENSMICG00000015668	4 retrocopies	retro_mmur_564, retro_mmur_60, retro_mmur_853, retro_mmur_994,
Myotis lucifugus	ENSMLUG00000010926	4 retrocopies	retro_mluc_1055, retro_mluc_1989, retro_mluc_215, retro_mluc_529,
Macaca mulatta	ENSMMUG00000004633	20 retrocopies	retro_mmul_1003, retro_mmul_1115, retro_mmul_1143, retro_mmul_1303, retro_mmul_1341, retro_mmul_1482, retro_mmul_1568, retro_mmul_1624, retro_mmul_1799, retro_mmul_1957, retro_mmul_2106, retro_mmul_2425, retro_mmul_2451, retro_mmul_2469, retro_mmul_2484, retro_mmul_2526, retro_mmul_267, retro_mmul_399, retro_mmul_514, retro_mmul_597,
Monodelphis domestica	ENSMODG00000005735	7 retrocopies	retro_mdom_1257, retro_mdom_1508, retro_mdom_1883, retro_mdom_1952, retro_mdom_587, retro_mdom_698, retro_mdom_831,
Mustela putorius furo	ENSMPUG00000011606	2 retrocopies	retro_mputfur_138, retro_mputfur_26,
Mus musculus	ENSMUSG00000015217	1 retrocopy	retro_mmus_273,
Oryctolagus cuniculus	ENSOCUG00000005986	7 retrocopies	retro_ocun_1033, retro_ocun_1913, retro_ocun_1914, retro_ocun_534, retro_ocun_568, retro_ocun_891, retro_ocun_931,
Otolemur garnettii	ENSOGAG00000001773	19 retrocopies	retro_ogar_1318, retro_ogar_1647, retro_ogar_1728, retro_ogar_187, retro_ogar_1930, retro_ogar_204, retro_ogar_2076, retro_ogar_2530, retro_ogar_2591, retro_ogar_2678, retro_ogar_2743, retro_ogar_2983, retro_ogar_3127, retro_ogar_3371, retro_ogar_343, retro_ogar_3433, retro_ogar_3479, retro_ogar_3513, retro_ogar_65,
Procavia capensis	ENSPCAG00000001945	1 retrocopy	retro_pcap_328 ,
Procavia capensis	ENSPCAG00000002201	2 retrocopies	retro_pcap_256, retro_pcap_432,
Pteropus vampyrus	ENSPVAG00000000219	1 retrocopy	retro_pvam_356,
Rattus norvegicus	ENSRNOG00000011096	4 retrocopies	retro_rnor_1049, retro_rnor_2303, retro_rnor_2359, retro_rnor_2363,
Rattus norvegicus	ENSRNOG00000050910	5 retrocopies	retro_rnor_1956, retro_rnor_2516, retro_rnor_2625, retro_rnor_720, retro_rnor_954,
Sarcophilus harrisii	ENSSHAG00000002916	2 retrocopies	retro_shar_139, retro_shar_316,
Sus scrofa	ENSSSCG00000012745	3 retrocopies	retro_sscr_1094, retro_sscr_466, retro_sscr_467,
Ictidomys tridecemlineatus	ENSSTOG00000023908	6 retrocopies	retro_itri_1366, retro_itri_1527, retro_itri_1655, retro_itri_1749, retro_itri_777, retro_itri_909,