RetrogeneDB ID: retro_cpor_1392

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:21235380..21235877(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTP4A1
• Ensembl ID: ENSCPOG00000025759
• Aliases: None
• Description: None

Sequence

>retro_cpor_1392
CCGAGCTCCTATGAAGGTAAGCATAAGAGCATAAGATTCCCTATTATACACAGTTCAAGCAATGCAACCTTAAACGAATT
CATAGAGGATCTTAAATATGGAATTACTACACTAGGAAGAAAATGTGAAGCAGCTCAACACACTGCTCTTTGTAGAGAAA
GAAGGCATTCATGTTCTCCATTGGCCTTTCAAGGGTGGTGTACTTTGTTCAATTAGAGTGTTAATGACTGGTTAAATCTT
GTAAAAATTAAGTTTTGTGAAAAAACCTGGTTGTTGAGTTGCTGTCCAGTGTGTTTTAGGCTTGGGAGAGCTCCAGTGCT
TGTTGTTGTACCATTAATTGAAGGTGGAATGACATTCCAAGATGCAGTACAGTTTGTAAGACCAAAGCAGCATGAAACTT
TTAAAAGCAAGCAGCTTTTGTATTTGTAGAAACATTGCCTTAAAATGCAACTGTGCCTCAAAGACTTTAATAGTTAAGAA
AGAACTGCTGTGTACAA

Alignment

ORF - retro_cpor_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.3 %
• Parental protein coverage: 96.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PAPVEVTYKSMRFLITHNPTNATLNKFIEELKKYGVTTIVRVCEATYDTTL-VEKEGIHVFDWPFDDGAP
          P...E...KS.RF.I.H...NATLN.FIE.LK.YG.TT..R.CEA...T.L.VEKEGIHV..WPF..G..
Retrocopy PSSYEGKHKSIRFPIIHSSSNATLNEFIEDLK-YGITTLGRKCEAAQHTAL>VEKEGIHVLHWPFKGGVL

Parental  PSNQI-VDDWLNLVKIKFRE-EPGCCIAVHCVAG-LGRAPVLVALALIEGGMKYEDAVQFIRQKRRGAFN
          .S....V.DWLNLVKIKF.E..PGC..AV.CV.G.LGRAPVLV...LIEGGM...DAVQF.R.K....F.
Retrocopy CSIRV<VNDWLNLVKIKFCE>KPGC*VAVQCVLG<LGRAPVLVVVPLIEGGMTFQDAVQFVRPKQHETFK

Parental  SKQLLYLEKYRPKMRLRFKDSNG-HRNNCCMQ
          SKQLLYL.K...KM.L..KD.N...R.NCC.Q
Retrocopy SKQLLYL*KHCLKMQLCLKDFNS<LRKNCCVQ

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	27.44 RPM
SRP017611_kidney	0.00 RPM	23.45 RPM
SRP017611_liver	0.00 RPM	21.28 RPM
SRP040447_lung	0.00 RPM	27.29 RPM
SRP040447_skeletal_muscle	0.00 RPM	37.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1392 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1392 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 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002275	3 retrocopies	retro_btau_1051, retro_btau_1186, retro_btau_859,
Cavia porcellus	ENSCPOG00000025759	5 retrocopies	retro_cpor_1137, retro_cpor_1233, retro_cpor_1392 , retro_cpor_552, retro_cpor_58,
Echinops telfairi	ENSETEG00000008183	6 retrocopies	retro_etel_1485, retro_etel_1681, retro_etel_1698, retro_etel_18, retro_etel_2153, retro_etel_668,
Latimeria chalumnae	ENSLACG00000007183	1 retrocopy	retro_lcha_90,
Loxodonta africana	ENSLAFG00000006572	8 retrocopies	retro_lafr_1054, retro_lafr_1120, retro_lafr_1133, retro_lafr_328, retro_lafr_670, retro_lafr_7, retro_lafr_780, retro_lafr_939,
Myotis lucifugus	ENSMLUG00000001162	1 retrocopy	retro_mluc_264,
Macaca mulatta	ENSMMUG00000002777	1 retrocopy	retro_mmul_1720,
Monodelphis domestica	ENSMODG00000018701	5 retrocopies	retro_mdom_1630, retro_mdom_1864, retro_mdom_363, retro_mdom_729, retro_mdom_927,
Nomascus leucogenys	ENSNLEG00000000440	6 retrocopies	retro_nleu_1111, retro_nleu_1159, retro_nleu_1681, retro_nleu_169, retro_nleu_407, retro_nleu_893,
Oryctolagus cuniculus	ENSOCUG00000006311	4 retrocopies	retro_ocun_225, retro_ocun_226, retro_ocun_24, retro_ocun_26,
Ochotona princeps	ENSOPRG00000004938	4 retrocopies	retro_opri_246, retro_opri_511, retro_opri_692, retro_opri_973,
Pongo abelii	ENSPPYG00000016743	5 retrocopies	retro_pabe_2058, retro_pabe_255, retro_pabe_2660, retro_pabe_3732, retro_pabe_721,
Rattus norvegicus	ENSRNOG00000011771	4 retrocopies	retro_rnor_1591, retro_rnor_2798, retro_rnor_494, retro_rnor_827,
Rattus norvegicus	ENSRNOG00000046370	4 retrocopies	retro_rnor_2349, retro_rnor_2868, retro_rnor_612, retro_rnor_971,
Tupaia belangeri	ENSTBEG00000009956	14 retrocopies	retro_tbel_1216, retro_tbel_1392, retro_tbel_2167, retro_tbel_2236, retro_tbel_23, retro_tbel_2549, retro_tbel_2570, retro_tbel_2611, retro_tbel_3144, retro_tbel_3295, retro_tbel_3424, retro_tbel_4074, retro_tbel_4123, retro_tbel_869,
Tursiops truncatus	ENSTTRG00000004129	6 retrocopies	retro_ttru_34, retro_ttru_450, retro_ttru_571, retro_ttru_642, retro_ttru_643, retro_ttru_69,
Vicugna pacos	ENSVPAG00000004277	9 retrocopies	retro_vpac_167, retro_vpac_201, retro_vpac_275, retro_vpac_427, retro_vpac_476, retro_vpac_496, retro_vpac_535, retro_vpac_560, retro_vpac_583,