RetrogeneDB ID: retro_cpor_666

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_22:7374907..7375497(+)
• Located in intron of: ENSCPOG00000003697

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPMT
• Ensembl ID: ENSCPOG00000005295
• Aliases: None
• Description: None

Sequence

>retro_cpor_666
CATTTGGATACTTTTCATAAAGGTGAGAGTGGACCAAGACTGTTTTTTCCCCTTTGCGGAAAAGCAGTGGAGAGGAAATG
ATTAGCAGACACAGTGCAAATCACACTGGGACACAGTGTAGCTGGTGTCAAAATCAGTGCTTGGGATACAGGAATTTTTA
TGGAGCAGAATCTCTCTTCCTCAGAAGAGCCAATCACTGAAATTCCTGACACAAAAATGTTTAAGAAGTTTTCAGGGAAT
ATTTTACTGTACTATTGCAGCATTTTCCATCTTTCCAGAGCAAATATTGGTAAATTTGACAGGATTTTGAATAGAGGAGC
ATTAATCTCTGTGAATCCAGGTGACCTTGGACGCTGGACAGACGTAATGCTGTTCCTACGGAGAACAGGATTTCTCTACC
TTAAGTCTGTTTTCTCTTATGATCCAAGAAAACATGGAGCCACACCATTTTATGTTTCAGATTTTGAAATTCAAACACTC
TTTGGTACAAAGTACAATGTTTTTTGCCTTGAAAAAGTTGCTACTATTGAGAAATCAAAAAATTGGGAACTCACTAGTTT
TTTGAAAAATTTTATCTACTGAAAGAAAAG

Alignment

ORF - retro_cpor_666 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.61 %
• Parental protein coverage: 79.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HLDTFLKGESGLRVFFPLCGKAVEMKWFADLGHSVVGVEISELGIREF----FMEQNLTYSEEPITEIPG
          HLDTF.KGESG.R.FFPLCGKAVE.K..AD......G.......I.......FMEQNL..SEEPITEIP.
Retrocopy HLDTFHKGESGPRLFFPLCGKAVERK*LADTVQITLGHSVAGVKISAWDTGIFMEQNLSSSEEPITEIPD

Parental  AKVFKSSSGNILLYCCNIFDLPRANVGKFDRIWDRGAFVAVNPSDRGRYAGVMLSLLRKGFLYLMSVFSY
          .K.FK..SGNILLY.C.IF.L.RAN.GKFDRI..RGA...VNP.D.GR...VML.L.R.GFLYL.SVFSY
Retrocopy TKMFKKFSGNILLYYCSIFHLSRANIGKFDRILNRGALISVNPGDLGRWTDVMLFLRRTGFLYLKSVFSY

Parental  DPTKYEGPPFYVPHSEIQALFGTKCNILCLEKVDALEK-LNVGSDYFF-EKLYLLTEK
          DP.K....PFYV...EIQ.LFGTK.N..CLEKV...EK....G....F.EK.YLL.EK
Retrocopy DPRKHGATPFYVSDFEIQTLFGTKYNVFCLEKVATIEK>QKIGNSLVF>EKFYLLKEK

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	1.90 RPM
SRP017611_kidney	0.10 RPM	1.47 RPM
SRP017611_liver	0.00 RPM	0.83 RPM
SRP040447_lung	0.03 RPM	1.61 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.22 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_666 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_666 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 14 parental genes, and 61 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008676	27 retrocopies	retro_chof_1029, retro_chof_1047, retro_chof_1184, retro_chof_1209, retro_chof_1425, retro_chof_1451, retro_chof_1483, retro_chof_1498, retro_chof_168, retro_chof_1830, retro_chof_1946, retro_chof_195, retro_chof_2039, retro_chof_2203, retro_chof_2543, retro_chof_2562, retro_chof_2649, retro_chof_330, retro_chof_503, retro_chof_626, retro_chof_637, retro_chof_684, retro_chof_743, retro_chof_761, retro_chof_78, retro_chof_79, retro_chof_921,
Callithrix jacchus	ENSCJAG00000006906	2 retrocopies	retro_cjac_1617, retro_cjac_4192,
Cavia porcellus	ENSCPOG00000005295	1 retrocopy	retro_cpor_666 ,
Dasypus novemcinctus	ENSDNOG00000004842	1 retrocopy	retro_dnov_965,
Homo sapiens	ENSG00000137364	4 retrocopies	retro_hsap_1884, retro_hsap_2781, retro_hsap_4835, retro_hsap_4868,
Gorilla gorilla	ENSGGOG00000016155	4 retrocopies	retro_ggor_1381, retro_ggor_1938, retro_ggor_3014, retro_ggor_3041,
Loxodonta africana	ENSLAFG00000011632	1 retrocopy	retro_lafr_438,
Macaca mulatta	ENSMMUG00000016627	3 retrocopies	retro_mmul_1445, retro_mmul_2576, retro_mmul_2609,
Mus musculus	ENSMUSG00000021376	1 retrocopy	retro_mmus_2738,
Nomascus leucogenys	ENSNLEG00000001548	4 retrocopies	retro_nleu_1806, retro_nleu_2001, retro_nleu_2710, retro_nleu_682,
Oryctolagus cuniculus	ENSOCUG00000003854	2 retrocopies	retro_ocun_1255, retro_ocun_1370,
Otolemur garnettii	ENSOGAG00000007738	2 retrocopies	retro_ogar_1972, retro_ogar_701,
Pongo abelii	ENSPPYG00000016263	4 retrocopies	retro_pabe_1563, retro_pabe_2235, retro_pabe_3758, retro_pabe_3786,
Pan troglodytes	ENSPTRG00000017756	5 retrocopies	retro_ptro_1265, retro_ptro_1882, retro_ptro_3217, retro_ptro_3218, retro_ptro_3243,