RetrogeneDB ID: retro_cjac_1788

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:48881982..48882325(+)
• Located in intron of: ENSCJAG00000015624

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000020461
• Aliases: None
• Description: None

Sequence

>retro_cjac_1788
GCCAATCAGTCTCAGGGGATTCAGCAGCTGCTGCAGACCAAGACGCAGCCCCTGAGAAGGTGTCCAAGTGTGAGCAAAAA
ACCTAGAGGCTGAATGAAGCAGGCCAAGGAAGCAGCTGAGGCTGAAACTGAACAGCACTGCCTGCAGGGGGAGAAAGAGT
TCAAGACCAAGGAAGCCGTTCCCTGGAATCCCACAGCAGCCATGGCACCTCCTACAGGAGGATCAGAGGAAGAAAACCAG
CCTCCAGACCTACTTCCAGCAGAATGGGGGTGAAGGCTTGGATAGCCTCCTGGCTTTTGTCTGTGACACCTGGACAGAAA
TCCATGAAAACTGCTGCGTAAAT

Alignment

ORF - retro_cjac_1788 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.54 %
• Parental protein coverage: 98.31 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASQSQGIQQLLQAEKRAAEKVSEARKRKNRRLKQAKEEAQAEIEQYRLQREKEFKAKEAA-ALGSHGSCS
          A.QSQGIQQLLQ.............K......KQAKE.A.AE.EQ..LQ.EKEFK.KEA...L.SH.S..
Retrocopy ANQSQGIQQLLQTKTQPLRRCPSVSKKPRG*MKQAKEAAEAETEQHCLQGEKEFKTKEAV<SLESHSSHG

Parental  TE-VEKETQEKMTILQTYFRQNRDEVLDNLLAFVCDIRPEIHENYRIN
          T.........K.T.LQTYF.QN..E.LD.LLAFVCD...EIHEN...N
Retrocopy TS<LQEDQRKK-TSLQTYFQQNGGEGLDSLLAFVCDTWTEIHENCCVN

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	81.56 RPM
SRP051959_heart	0.11 RPM	54.02 RPM
SRP051959_kidney	0.87 RPM	181.13 RPM
SRP051959_liver	0.00 RPM	88.51 RPM
SRP051959_lung	0.13 RPM	78.56 RPM
SRP051959_lymph_node	0.00 RPM	83.01 RPM
SRP051959_skeletal_muscle	0.74 RPM	70.86 RPM
SRP051959_spleen	0.04 RPM	89.94 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1788 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1788 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1788 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_2215
Macaca mulatta	retro_mmul_2046

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 89 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012509	3 retrocopies	retro_amel_1053, retro_amel_376, retro_amel_999,
Callithrix jacchus	ENSCJAG00000020461	3 retrocopies	retro_cjac_1788 , retro_cjac_2513, retro_cjac_76,
Cavia porcellus	ENSCPOG00000000763	5 retrocopies	retro_cpor_1523, retro_cpor_204, retro_cpor_688, retro_cpor_742, retro_cpor_852,
Dasypus novemcinctus	ENSDNOG00000008083	15 retrocopies	retro_dnov_1173, retro_dnov_1447, retro_dnov_1475, retro_dnov_1504, retro_dnov_1588, retro_dnov_1645, retro_dnov_193, retro_dnov_1998, retro_dnov_2179, retro_dnov_218, retro_dnov_2416, retro_dnov_245, retro_dnov_336, retro_dnov_479, retro_dnov_790,
Dipodomys ordii	ENSDORG00000014850	5 retrocopies	retro_dord_434, retro_dord_466, retro_dord_614, retro_dord_640, retro_dord_749,
Equus caballus	ENSECAG00000011155	1 retrocopy	retro_ecab_816,
Echinops telfairi	ENSETEG00000008080	3 retrocopies	retro_etel_350, retro_etel_594, retro_etel_996,
Felis catus	ENSFCAG00000000160	2 retrocopies	retro_fcat_1614, retro_fcat_402,
Homo sapiens	ENSG00000136888	3 retrocopies	retro_hsap_3198, retro_hsap_4049, retro_hsap_763,
Gorilla gorilla	ENSGGOG00000004011	4 retrocopies	retro_ggor_1331, retro_ggor_2215, retro_ggor_2717, retro_ggor_632,
Loxodonta africana	ENSLAFG00000013437	2 retrocopies	retro_lafr_1002, retro_lafr_39,
Microcebus murinus	ENSMICG00000015368	3 retrocopies	retro_mmur_1217, retro_mmur_1259, retro_mmur_755,
Myotis lucifugus	ENSMLUG00000008657	2 retrocopies	retro_mluc_373, retro_mluc_839,
Macaca mulatta	ENSMMUG00000004899	4 retrocopies	retro_mmul_1783, retro_mmul_2018, retro_mmul_2046, retro_mmul_331,
Monodelphis domestica	ENSMODG00000019574	1 retrocopy	retro_mdom_1675,
Mustela putorius furo	ENSMPUG00000001653	3 retrocopies	retro_mputfur_1338, retro_mputfur_922, retro_mputfur_994,
Mus musculus	ENSMUSG00000039105	5 retrocopies	retro_mmus_2028, retro_mmus_2784, retro_mmus_2787, retro_mmus_3316, retro_mmus_819,
Nomascus leucogenys	ENSNLEG00000016833	2 retrocopies	retro_nleu_1151, retro_nleu_3045,
Oryctolagus cuniculus	ENSOCUG00000026252	3 retrocopies	retro_ocun_1411, retro_ocun_368, retro_ocun_639,
Otolemur garnettii	ENSOGAG00000010103	3 retrocopies	retro_ogar_1824, retro_ogar_2822, retro_ogar_342,
Pan troglodytes	ENSPTRG00000021290	2 retrocopies	retro_ptro_2248, retro_ptro_2744,
Pteropus vampyrus	ENSPVAG00000008334	1 retrocopy	retro_pvam_1432,
Rattus norvegicus	ENSRNOG00000008163	2 retrocopies	retro_rnor_1246, retro_rnor_676,
Ictidomys tridecemlineatus	ENSSTOG00000015857	5 retrocopies	retro_itri_1102, retro_itri_1235, retro_itri_1281, retro_itri_1340, retro_itri_1669,
Tupaia belangeri	ENSTBEG00000010985	2 retrocopies	retro_tbel_2147, retro_tbel_786,
Tarsius syrichta	ENSTSYG00000011474	3 retrocopies	retro_tsyr_1865, retro_tsyr_2141, retro_tsyr_614,
Tursiops truncatus	ENSTTRG00000015203	2 retrocopies	retro_ttru_125, retro_ttru_480,