RetrogeneDB ID: retro_cjac_2296

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:169495583..169496147(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18
• Ensembl ID: ENSCJAG00000000377
• Aliases: None
• Description: ribosomal protein L18 [Source:HGNC Symbol;Acc:10310]

Sequence

>retro_cjac_2296
ATGGGAGCTGACATCTGTCACAACCAGGACCGAAAGGTTCAGCGCAAGGAGCCCAAGAGCCAGGACATCTACCTGAGGCT
GTTGGTCAAGACTGTACAGGTTTCTGGCCAGGCGAACCAACTCCACATTCAATCAAGTTGTGCTGAAGAGGTTGTTTATG
AGTTGCACCAATCAGCCACCTCTGTTCCCTTTCCGGATGATCTGGAAGATGAAGATTCCTGGCCGGGGAAACAAAAAGGC
CGTGGTTGTGGGGACCACAGCGGGTGACGTGCGGGTTCAGGAGGTGCCTGAACTGAAGGTGTGTGCGCTGCGTGTGACCA
GCCGGACCAGCAGCCGTGTGCTCAAGGCGGGGGGCAAATCCGCACTTTGGACCAGCTGACCCTGGACTTCCCCAAGGGTT
GCGGCACCATCCTGTTCTCCGGTCCTCACAAGGGCTGAGAGGTATCCCGGCATTTCGGCAAGGCCCCAGGAACCCCGCAC
AGCCACACCAAACCCTAGGTCTGCTCCAAGGGCCGGAAGTTCGAGTGGACCAGAGGCCGAGGGGCCGGCCAAGGCTATAA
AAAC

Alignment

ORF - retro_cjac_2296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MGVDIRHNKDRKVRRKEPKSQDIYLRLLVK-LYRFLARRTNSTFNQVVLKRLFMSRTNRPPLSLSRMIRK
          MG.DI.HN.DRKV.RKEPKSQDIYLRLLVK.LYRFLARRTNSTFNQVVLKRLFMS.TN.PPL...RMI.K
Retrocopy MGADICHNQDRKVQRKEPKSQDIYLRLLVK>LYRFLARRTNSTFNQVVLKRLFMSCTNQPPLFPFRMIWK

Parental  MKLPGRENKTAVVVGTVTDDVRVQEVPKLKVCALRVTSRARSRILKAGGK-ILTFDQLALDSPKGCGTVL
          MK.PGR.NK.AVVVGT...DVRVQEVP.LKVCALRVTSR..SR.LKAGGK.I.T.DQL.LD.PKGCGT.L
Retrocopy MKIPGRGNKKAVVVGTTAGDVRVQEVPELKVCALRVTSRTSSRVLKAGGK<IRTLDQLTLDFPKGCGTIL

Parental  LSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGRRASRGYKN
          .SGP.KG.EV.RHFGKAPGTPHSHTKP.V.SKGRKFE..RGR.A..GYKN
Retrocopy FSGPHKG*EVSRHFGKAPGTPHSHTKP*VCSKGRKFEWTRGRGAGQGYKN

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
SRP051959_colon	0.00 RPM	107.96 RPM
SRP051959_heart	0.02 RPM	65.09 RPM
SRP051959_kidney	0.00 RPM	77.14 RPM
SRP051959_liver	0.00 RPM	97.10 RPM
SRP051959_lung	0.00 RPM	89.21 RPM
SRP051959_lymph_node	0.00 RPM	138.74 RPM
SRP051959_skeletal_muscle	0.00 RPM	75.56 RPM
SRP051959_spleen	0.00 RPM	97.77 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2296 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2296 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2296 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 105 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009140	6 retrocopies	retro_chof_1408, retro_chof_1668, retro_chof_1697, retro_chof_2025, retro_chof_427, retro_chof_436,
Callithrix jacchus	ENSCJAG00000000377	4 retrocopies	retro_cjac_1659, retro_cjac_2114, retro_cjac_2296 , retro_cjac_529,
Felis catus	ENSFCAG00000008652	4 retrocopies	retro_fcat_1055, retro_fcat_1268, retro_fcat_1596, retro_fcat_718,
Homo sapiens	ENSG00000063177	11 retrocopies	retro_hsap_1073, retro_hsap_1202, retro_hsap_1331, retro_hsap_1617, retro_hsap_1706, retro_hsap_3235, retro_hsap_3794, retro_hsap_3895, retro_hsap_4001, retro_hsap_4111, retro_hsap_772,
Gorilla gorilla	ENSGGOG00000024878	7 retrocopies	retro_ggor_1038, retro_ggor_1280, retro_ggor_2200, retro_ggor_2550, retro_ggor_2624, retro_ggor_847, retro_ggor_937,
Macropus eugenii	ENSMEUG00000000640	1 retrocopy	retro_meug_1568,
Macaca mulatta	ENSMMUG00000022158	3 retrocopies	retro_mmul_32, retro_mmul_55, retro_mmul_92,
Monodelphis domestica	ENSMODG00000014099	1 retrocopy	retro_mdom_906,
Mustela putorius furo	ENSMPUG00000003891	4 retrocopies	retro_mputfur_135, retro_mputfur_1410, retro_mputfur_529, retro_mputfur_974,
Nomascus leucogenys	ENSNLEG00000004537	11 retrocopies	retro_nleu_1124, retro_nleu_1136, retro_nleu_1410, retro_nleu_1799, retro_nleu_2006, retro_nleu_2380, retro_nleu_2464, retro_nleu_2597, retro_nleu_547, retro_nleu_577, retro_nleu_976,
Otolemur garnettii	ENSOGAG00000003562	16 retrocopies	retro_ogar_1167, retro_ogar_1474, retro_ogar_1563, retro_ogar_1753, retro_ogar_1978, retro_ogar_2394, retro_ogar_2419, retro_ogar_2527, retro_ogar_2613, retro_ogar_2833, retro_ogar_3319, retro_ogar_3456, retro_ogar_3458, retro_ogar_3459, retro_ogar_492, retro_ogar_996,
Oreochromis niloticus	ENSONIG00000006539	1 retrocopy	retro_onil_43,
Pan troglodytes	ENSPTRG00000011245	10 retrocopies	retro_ptro_1084, retro_ptro_1155, retro_ptro_2187, retro_ptro_2574, retro_ptro_2649, retro_ptro_2790, retro_ptro_540, retro_ptro_730, retro_ptro_822, retro_ptro_908,
Rattus norvegicus	ENSRNOG00000021035	14 retrocopies	retro_rnor_1068, retro_rnor_1072, retro_rnor_1154, retro_rnor_1186, retro_rnor_1337, retro_rnor_1359, retro_rnor_2174, retro_rnor_2224, retro_rnor_2847, retro_rnor_2890, retro_rnor_516, retro_rnor_685, retro_rnor_856, retro_rnor_857,
Sarcophilus harrisii	ENSSHAG00000006564	2 retrocopies	retro_shar_571, retro_shar_659,
Sus scrofa	ENSSSCG00000025928	5 retrocopies	retro_sscr_1028, retro_sscr_118, retro_sscr_836, retro_sscr_864, retro_sscr_925,
Ictidomys tridecemlineatus	ENSSTOG00000012258	5 retrocopies	retro_itri_261, retro_itri_323, retro_itri_828, retro_itri_853, retro_itri_957,