RetrogeneDB ID: retro_pcap_432

Retrocopy location

• Organism: Hyrax (Procavia capensis)
• Coordinates: scaffold_85558:417..1000(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB1
• Ensembl ID: ENSPCAG00000002201
• Aliases: None
• Description: high mobility group box 1 [Source:HGNC Symbol;Acc:4983]

Sequence

>retro_pcap_432
ATGGGCAAAACAGACCCCAACAAGCTGCGGGGCAAAATGCCCTCGTACGCCTTCTTTGTGCAGACCTGCCAGTAAGAGTA
CAAAAAGAAACACCCGGACTCCTCCGTCACTTCCGCAGAGTTCTCCAAGAAGTGTTCCGAGAAAACAAGGTCTGCCAAGA
AAAAGTCCAAGTTTGAAGATAAAGCCAAAAAGTGACAAGGCTCACTATGACAGGGAGATGAAAAACTACGTTCCTCCCAA
CGGTCACAGGAAAGGACAGAAAAAAGATCCCAATGCTCCCTAAAGGCCACTATCTGCCTTCTTCCTGTTTTGCTCTGAAC
ATCCCCCGAAGATCAAAAGTGAACACCGAGGTCTATCCATTGGGGATACTGTGAAAAAACTGGATGAAATATGGTCTGAA
CAATCAGCCAAAGATAAACAACCGTATGAACAGAAAGCAGCCAAGCTAAAGGAGAAATATGAAAAGGATATTGCCCTATA
CTGTGCCAAGGGCAAAAGTGAAGCAGGAAAGAAGGGTTTTGGTAGGTCAACAGGCTGAAAGAAGAATGAACCAGAAGGTG
AGGAAGAAGATGAAGATGAAGAG

Alignment

ORF - retro_pcap_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.99 %
• Parental protein coverage: 91.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK-ADKA
          MGK.DP.K.RGKM.SYAFFVQTC..E.KKKHPD.SV...EFSKKCSE..KT.SAK.K.KFED.AK..DKA
Retrocopy MGKTDPNKLRGKMPSYAFFVQTCQ*EYKKKHPDSSVTSAEFSKKCSE--KTRSAKKKSKFEDKAK>SDKA

Parental  RYEREMKTYIPPKGETK-KFKDPNAPKRPPSAFFLFCYEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAAD
          .Y.REMK.Y.PP.G..K...KDPNAP.RP.SAFFLFC.E..PKIK.EH.GLSIGD..KKL.E.W....A.
Retrocopy HYDREMKNYVPPNGHRKGQKKDPNAP*RPLSAFFLFCSEHPPKIKSEHRGLSIGDTVKKLDEIWSEQSAK

Parental  DKQPYEKKAAKLKEKYEKDIAAYRAKGKPDAAKKGVVKAEKSKKKKEEEEDEEDEED
          DKQPYE.KAAKLKEKYEKDIA.Y.AKGK..A.KKG.......KK...E.E.E...E.
Retrocopy DKQPYEQKAAKLKEKYEKDIALYCAKGKSEAGKKGFGRSTG*KKNEPEGEEEDEDEE

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_432 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 13 parental genes, and 159 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006597	13 retrocopies	retro_cfam_1088, retro_cfam_1102, retro_cfam_1387, retro_cfam_1628, retro_cfam_1765, retro_cfam_1831, retro_cfam_1980, retro_cfam_242, retro_cfam_280, retro_cfam_467, retro_cfam_495, retro_cfam_521, retro_cfam_528,
Homo sapiens	ENSG00000189403	37 retrocopies	retro_hsap_1230, retro_hsap_1357, retro_hsap_1504, retro_hsap_1589, retro_hsap_1608, retro_hsap_176, retro_hsap_1832, retro_hsap_1954, retro_hsap_2103, retro_hsap_2192, retro_hsap_2219, retro_hsap_2228, retro_hsap_2340, retro_hsap_2490, retro_hsap_2552, retro_hsap_2613, retro_hsap_2660, retro_hsap_2858, retro_hsap_2947, retro_hsap_3317, retro_hsap_3340, retro_hsap_3592, retro_hsap_3615, retro_hsap_3666, retro_hsap_382, retro_hsap_3942, retro_hsap_4003, retro_hsap_4109, retro_hsap_4309, retro_hsap_4669, retro_hsap_470, retro_hsap_4738, retro_hsap_4832, retro_hsap_525, retro_hsap_554, retro_hsap_758, retro_hsap_933,
Gorilla gorilla	ENSGGOG00000026764	23 retrocopies	retro_ggor_1057, retro_ggor_1212, retro_ggor_1421, retro_ggor_1596, retro_ggor_1637, retro_ggor_1662, retro_ggor_1735, retro_ggor_1777, retro_ggor_1856, retro_ggor_1951, retro_ggor_1977, retro_ggor_213, retro_ggor_2422, retro_ggor_2441, retro_ggor_2478, retro_ggor_259, retro_ggor_2897, retro_ggor_3013, retro_ggor_388, retro_ggor_448, retro_ggor_483, retro_ggor_753, retro_ggor_964,
Macropus eugenii	ENSMEUG00000001380	2 retrocopies	retro_meug_1591, retro_meug_825,
Macaca mulatta	ENSMMUG00000023399	3 retrocopies	retro_mmul_2079, retro_mmul_320, retro_mmul_385,
Monodelphis domestica	ENSMODG00000009238	14 retrocopies	retro_mdom_1088, retro_mdom_1144, retro_mdom_1228, retro_mdom_1689, retro_mdom_1727, retro_mdom_1819, retro_mdom_2007, retro_mdom_2024, retro_mdom_3, retro_mdom_434, retro_mdom_548, retro_mdom_72, retro_mdom_760, retro_mdom_958,
Ochotona princeps	ENSOPRG00000003507	8 retrocopies	retro_opri_1030, retro_opri_1150, retro_opri_1209, retro_opri_140, retro_opri_279, retro_opri_42, retro_opri_553, retro_opri_706,
Procavia capensis	ENSPCAG00000001945	1 retrocopy	retro_pcap_328,
Procavia capensis	ENSPCAG00000002201	2 retrocopies	retro_pcap_256, retro_pcap_432 ,
Pongo abelii	ENSPPYG00000005546	35 retrocopies	retro_pabe_1023, retro_pabe_1125, retro_pabe_1254, retro_pabe_1334, retro_pabe_1500, retro_pabe_159, retro_pabe_1724, retro_pabe_1831, retro_pabe_1973, retro_pabe_1997, retro_pabe_2070, retro_pabe_2089, retro_pabe_2194, retro_pabe_222, retro_pabe_2313, retro_pabe_2362, retro_pabe_2406, retro_pabe_2444, retro_pabe_264, retro_pabe_2732, retro_pabe_2751, retro_pabe_2752, retro_pabe_2777, retro_pabe_2953, retro_pabe_2966, retro_pabe_3008, retro_pabe_3365, retro_pabe_3523, retro_pabe_3684, retro_pabe_3757, retro_pabe_452, retro_pabe_511, retro_pabe_522, retro_pabe_761, retro_pabe_762,
Pteropus vampyrus	ENSPVAG00000001431	6 retrocopies	retro_pvam_1156, retro_pvam_154, retro_pvam_429, retro_pvam_508, retro_pvam_774, retro_pvam_960,
Rattus norvegicus	ENSRNOG00000029813	1 retrocopy	retro_rnor_421,
Sorex araneus	ENSSARG00000004470	14 retrocopies	retro_sara_131, retro_sara_182, retro_sara_259, retro_sara_293, retro_sara_302, retro_sara_342, retro_sara_378, retro_sara_402, retro_sara_47, retro_sara_564, retro_sara_576, retro_sara_613, retro_sara_655, retro_sara_765,