RetrogeneDB ID: retro_cpor_1436

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_83:2413480..2414372(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GHITM
• Ensembl ID: ENSCPOG00000006432
• Aliases: None
• Description: None

Sequence

>retro_cpor_1436
CCAGCTTTCAGTGGCTCAACACCCAGCAGGCAATATGCCACCAGGTCAAGACTTGGACTCCCCCATGGGAAAACTGCCCA
GGAACCATTAATAGAATAAATGCATAAAATTGAACAAATCGGAAAATTCTTTGTTGTTGGAGAGGCTGCTGTTGATATTG
GAGCACTGTGCTACTACGGCATGGGCATGTCTAATGAGATAGTAATTGTAAAGGCTGTAATTTGGCCTCATTGTGTGAAG
GATAGGATACATTCCACGTATATGTCCTTAGCAGGACATATTTGTTTAGCAGCTTTGTCTGCCTTGACAGTAGCTAGAAG
TCCTGTTCTCATGAACTTCACAATGAAAGACTCTTTGGTGACGATTGGTGCAACTTTTGCAGCCATGATCAAACCTGGAA
TGCCAGTACAATCCACGTCCTTCTAATGGCACCCAGACAAAAAGAATCTTGCTTGGTTGTTCCACTCTTGTGTGATGGGG
GCAGTGGTGGATTCCTCTAACAAGAGGAGAGGTGGCCCTCTCCTCTTCAGAGCCATGTATTACGTAGCTGGCATGGGGGC
AGCCACATGTGCATCCAGTGAGAAGCTTCTGAATGTGGTAGCGCTCCTGGGTATGGGTTTGGATCTTGTCTCTGAGGCCT
CATGGAATCAATGTTTATTCCACCTATCACTATGGCTGATTACACTCTGTACACAGTGGCAGTGTAGGATAGGTTAGTTC
TCTTCAGCATGTTCCTTCTGCATGCTACTCAAAAAGTAATAAATGTGTAGAAATAACACCAGTGTATGGAGTTCAAAAAT
ATGATCTCATCAAAGCGATGCTGGCAATCTACGTAAATATTTTAAATGTATTCATATGAGTTGTAGTTATGCTGGCAACT
GGAGGTAACAAA

Alignment

ORF - retro_cpor_1436 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.5 %
• Parental protein coverage: 87.57 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PSREYATRSRFGIRRGKTAQELKEAAMEPSVEKAYKIEQLGKCFLAGGAAVGLGALCYYGLGMSNEIGAI
          P.....T.SR....R..........A.EP..E...KIEQ.GK.F..G.AAV..GALCYYG.GMSNEI..I
Retrocopy PAFSGSTPSRQYATRSRLGLPHGKTAQEPLIE*MHKIEQIGKFFVVGEAAVDIGALCYYGMGMSNEI-VI

Parental  EKAVVWPQYVKDRIHSTYMYLAGSVGFTALSALAVARSPVLMNFMMRGSLVTVGATFVAMIGAGMLVQSI
          .KAV.WP..VKDRIHSTYM.LAG.....ALSAL.VARSPVLMNF.M..SLVT.GATF.AMI..GM.VQS.
Retrocopy VKAVIWPHCVKDRIHSTYMSLAGHICLAALSALTVARSPVLMNFTMKDSLVTIGATFAAMIKPGMPVQST

Parental  PYEQQPGPKHLAWLLHSGVMGAVVAPLTILGG-PLLVRAAWYTAGIVGGLSTVAMCAPSEKFLNMGAPLG
          .....P..K.LAWL.HS.VMGAVV.......G.PLL.RA..Y.AG...G..T.A....SEK.LN..A.LG
Retrocopy SF*WHPDKKNLAWLFHSCVMGAVVDSSNKRRGGPLLFRAMYYVAGM--GAATCA---SSEKLLNVVALLG

Parental  VGLGLVFAAS-LGSMFIPPTTVAGSALYTVAVYGGLALFSMFLLHDTQKVI-KRAEITPVYGAQKFDPIN
          .GL.LV..AS...SMFIPP.T.A...LYTVAV...L.LFSMFLLH.TQKVI.K..EITPVYG.QK.D.I.
Retrocopy MGLDLVSEAS<MESMFIPPITMADYTLYTVAV*DRLVLFSMFLLHATQKVI<KCVEITPVYGVQKYDLIK

Parental  SMLAIYMDVLNIFMRVATMLAAGGNR
          .MLAIY...LN.F..V..MLA.GGN.
Retrocopy AMLAIYVNILNVFI*VVVMLATGGNK

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	0.00 RPM	66.89 RPM
SRP017611_kidney	0.00 RPM	286.01 RPM
SRP017611_liver	0.00 RPM	135.41 RPM
SRP040447_lung	0.03 RPM	84.49 RPM
SRP040447_skeletal_muscle	0.00 RPM	169.81 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1436 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1436 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 18 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009753	1 retrocopy	retro_amel_336,
Bos taurus	ENSBTAG00000032829	2 retrocopies	retro_btau_1689, retro_btau_779,
Choloepus hoffmanni	ENSCHOG00000001576	1 retrocopy	retro_chof_5,
Cavia porcellus	ENSCPOG00000006432	1 retrocopy	retro_cpor_1436 ,
Dasypus novemcinctus	ENSDNOG00000018880	5 retrocopies	retro_dnov_2426, retro_dnov_2514, retro_dnov_2524, retro_dnov_708, retro_dnov_812,
Dipodomys ordii	ENSDORG00000001109	1 retrocopy	retro_dord_184,
Echinops telfairi	ENSETEG00000001796	1 retrocopy	retro_etel_68,
Loxodonta africana	ENSLAFG00000009646	1 retrocopy	retro_lafr_388,
Macropus eugenii	ENSMEUG00000009861	3 retrocopies	retro_meug_1431, retro_meug_1806, retro_meug_798,
Microcebus murinus	ENSMICG00000011621	1 retrocopy	retro_mmur_692,
Monodelphis domestica	ENSMODG00000001693	3 retrocopies	retro_mdom_1008, retro_mdom_407, retro_mdom_886,
Oryctolagus cuniculus	ENSOCUG00000006093	1 retrocopy	retro_ocun_260,
Otolemur garnettii	ENSOGAG00000012120	1 retrocopy	retro_ogar_1287,
Rattus norvegicus	ENSRNOG00000013961	1 retrocopy	retro_rnor_2461,
Sus scrofa	ENSSSCG00000010345	1 retrocopy	retro_sscr_1102,
Tupaia belangeri	ENSTBEG00000016365	2 retrocopies	retro_tbel_1601, retro_tbel_2819,
Tarsius syrichta	ENSTSYG00000006367	1 retrocopy	retro_tsyr_4,
Drosophila melanogaster	FBgn0030263	1 retrocopy	retro_dmel_61,