RetrogeneDB ID: retro_cpor_1273

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_62:10611375..10611826(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPT1
• Ensembl ID: ENSCPOG00000009278
• Aliases: None
• Description: translationally-controlled tumor protein [Source:RefSeq peptide;Acc:NP_001166553]

Sequence

>retro_cpor_1273
GACCTCATCAGCCATGATGAGATATTCTTTGACATTTACAAGATCTGGGAGATTGTGGGTGGTCTGTGCTGGAGGTGGAG
AGCAAAGATGGTCTGTAGAACAGAGAGTAACACTGATGACTCACTCACTGGTGGAAATGCCAACCCTGAAGGCCCAGAGA
GCAGAGGCACCGAAAGTACAGAAGTCGCTGGTGTTGATATTGTCAGGAACCATCACTTGCTAGAAACCAGCTTCACCAAA
AGGCCTACAAGAAATACATCAAAGATTATATAAAATCAATCTGAGGCACACTTGAAGAACAAAGATCAGAAAGAGTAAAA
TCGCTTATGACAGGGGCTGCAGAACAAATTAAGGACATTCTTGCTCATTGCAAAAACCATCGGTTCTTTATTGATGAAAC
CTGAATTGCAGTGGCATGGTTGCTCTCCTGCACTGCAGTGAGGATGGTGTG

Alignment

ORF - retro_cpor_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.93 %
• Parental protein coverage: 87.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLISHDEMS-DIYKIREIADGLC-EVEGKMVSRTEGNIDDSLIGGNASAEGPEGEGTESTVITGVDIVMN
          DLISHDE...DIYKI.EI..GLC.....KMV.RTE.N.DDSL.GGNA..EGPE..GTEST...GVDIV.N
Retrocopy DLISHDEIFFDIYKIWEIVGGLCWRWRAKMVCRTESNTDDSLTGGNANPEGPESRGTESTEVAGVDIVRN

Parental  HHLQETSFTK-EAYKKYIKDYMKSIKGKLEEQRPERVKPFMTGAAEQIKHILANFKNYQFFIGA-NMNPD
          HHL.ETSFTK..AYKKYIKDY.KSI.G.LEEQR.ERVK..MTGAAEQIK.ILA..KN..FFI...N.N..
Retrocopy HHLLETSFTK<KAYKKYIKDYIKSI*GTLEEQRSERVKSLMTGAAEQIKDILAHCKNHRFFIDE<NLNCS

Parental  GMVALLDYREDGV
          GMVALL...EDGV
Retrocopy GMVALLHCSEDGV

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	377.83 RPM
SRP017611_kidney	0.00 RPM	916.22 RPM
SRP017611_liver	0.00 RPM	886.12 RPM
SRP040447_lung	0.03 RPM	996.93 RPM
SRP040447_skeletal_muscle	0.00 RPM	2302.05 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1273 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1273 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 82 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006531	2 retrocopies	retro_acar_156, retro_acar_58,
Cavia porcellus	ENSCPOG00000009278	12 retrocopies	retro_cpor_1053, retro_cpor_1215, retro_cpor_1273 , retro_cpor_206, retro_cpor_248, retro_cpor_340, retro_cpor_536, retro_cpor_583, retro_cpor_602, retro_cpor_697, retro_cpor_917, retro_cpor_968,
Dasypus novemcinctus	ENSDNOG00000000653	22 retrocopies	retro_dnov_1071, retro_dnov_1202, retro_dnov_1349, retro_dnov_1705, retro_dnov_2082, retro_dnov_2283, retro_dnov_2305, retro_dnov_237, retro_dnov_2412, retro_dnov_2531, retro_dnov_2687, retro_dnov_276, retro_dnov_342, retro_dnov_397, retro_dnov_417, retro_dnov_453, retro_dnov_71, retro_dnov_847, retro_dnov_870, retro_dnov_909, retro_dnov_934, retro_dnov_981,
Dipodomys ordii	ENSDORG00000008518	2 retrocopies	retro_dord_370, retro_dord_471,
Echinops telfairi	ENSETEG00000003091	3 retrocopies	retro_etel_1337, retro_etel_1546, retro_etel_248,
Latimeria chalumnae	ENSLACG00000004306	2 retrocopies	retro_lcha_24, retro_lcha_34,
Myotis lucifugus	ENSMLUG00000017709	1 retrocopy	retro_mluc_1332,
Monodelphis domestica	ENSMODG00000014940	2 retrocopies	retro_mdom_128, retro_mdom_9,
Mus musculus	ENSMUSG00000060126	8 retrocopies	retro_mmus_1643, retro_mmus_2193, retro_mmus_2354, retro_mmus_2862, retro_mmus_3264, retro_mmus_3371, retro_mmus_3483, retro_mmus_3496,
Oryctolagus cuniculus	ENSOCUG00000023692	2 retrocopies	retro_ocun_40, retro_ocun_75,
Procavia capensis	ENSPCAG00000016228	3 retrocopies	retro_pcap_245, retro_pcap_351, retro_pcap_357,
Pteropus vampyrus	ENSPVAG00000003191	15 retrocopies	retro_pvam_1069, retro_pvam_1116, retro_pvam_1142, retro_pvam_1145, retro_pvam_1252, retro_pvam_1266, retro_pvam_1290, retro_pvam_1322, retro_pvam_1387, retro_pvam_242, retro_pvam_369, retro_pvam_547, retro_pvam_585, retro_pvam_721, retro_pvam_801,
Rattus norvegicus	ENSRNOG00000001049	7 retrocopies	retro_rnor_115, retro_rnor_2464, retro_rnor_2706, retro_rnor_411, retro_rnor_886, retro_rnor_908, retro_rnor_958,
Sarcophilus harrisii	ENSSHAG00000001545	1 retrocopy	retro_shar_227,