RetrogeneDB ID: retro_cpor_384

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_14:14982993..14983351(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMGB3
• Ensembl ID: ENSCPOG00000000601
• Aliases: None
• Description: None

Sequence

>retro_cpor_384
ATGGCAAAAGGTGACCCCAAGAGACCAAAGAGCAAGATGACCACTTACCCTGCTTTATATAGATACACAGAGAGAAACAA
CAGAAGAAAAACCCAGAGGTCCCAGGCAGCTTTTCAGAATTTTCCATGAAGGGTTTTGAGAGGTAGAAGGCAATGTCTAG
AGAACAGAAATCTAAATTTGAAGAACTAGTAAATGTGGATAAAATATGATGTGGTCAGGAAATGAGGATTTATGGACCAG
CTAAGGGAGGTATCAAGAAATAGGGTCCTATATTCCCGAAAGATCACCATCTGGATTCTTCCTGTTCTGTTCATAAGTCC
ACCCTGAGACCAGATTCACAAGCCCCGTGACATCTCTA

Alignment

ORF - retro_cpor_384 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.92 %
• Parental protein coverage: 67.04 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKGDPKKPKGKMSAYAF-FVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKV
          MAKGDPK.PK.KM..Y...F....RE...KKNPEVP..F.EFS.K..ER.K.MS...KSKF.E....DK.
Retrocopy MAKGDPKRPKSKMTTYPA<FI*IHREKQQKKNPEVPGSFSEFSMKGFER*KAMSREQKSKFEELVNVDKI

Parental  RYDREMKDYGPAKGGKKKKDPNAPK-RPPSGFFLFCSEFRPKIKSTNPGISI
          ....EM..YGPAKGG.KK..P..PK.R.PSGFFLFCS...P....T.P..S.
Retrocopy *CGQEMRIYGPAKGGIKK*GPIFPK<RSPSGFFLFCS*VHPETRFTSPVTSL

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.12 RPM	5.29 RPM
SRP017611_kidney	0.00 RPM	2.30 RPM
SRP017611_liver	0.00 RPM	0.57 RPM
SRP040447_lung	0.00 RPM	1.01 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_384 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_384 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005150	2 retrocopies	retro_btau_190, retro_btau_38,
Choloepus hoffmanni	ENSCHOG00000005005	2 retrocopies	retro_chof_1891, retro_chof_2010,
Cavia porcellus	ENSCPOG00000000601	2 retrocopies	retro_cpor_1432, retro_cpor_384 ,
Cavia porcellus	ENSCPOG00000003552	4 retrocopies	retro_cpor_1100, retro_cpor_604, retro_cpor_890, retro_cpor_980,
Cavia porcellus	ENSCPOG00000003985	1 retrocopy	retro_cpor_69,
Echinops telfairi	ENSETEG00000015689	4 retrocopies	retro_etel_104, retro_etel_1272, retro_etel_385, retro_etel_465,
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,
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,
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,
Pteropus vampyrus	ENSPVAG00000000219	1 retrocopy	retro_pvam_356,
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,
Tupaia belangeri	ENSTBEG00000003068	18 retrocopies	retro_tbel_1002, retro_tbel_1230, retro_tbel_1579, retro_tbel_1700, retro_tbel_1819, retro_tbel_2543, retro_tbel_2730, retro_tbel_3261, retro_tbel_3476, retro_tbel_3623, retro_tbel_3781, retro_tbel_408, retro_tbel_410, retro_tbel_4203, retro_tbel_4209, retro_tbel_4299, retro_tbel_605, retro_tbel_698,
Tursiops truncatus	ENSTTRG00000000205	2 retrocopies	retro_ttru_1187, retro_ttru_372,
Vicugna pacos	ENSVPAG00000000096	2 retrocopies	retro_vpac_245, retro_vpac_434,