RetrogeneDB ID: retro_cjac_3110

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:11967739..11968215(-)
• Located in intron of: ENSCJAG00000008208

Retrocopy information

• Ensembl ID: ENSCJAG00000008220
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000015321
• Aliases: None
• Description: U1 small nuclear ribonucleoprotein C [Source:UniProtKB/TrEMBL;Acc:F6XG37]

Sequence

>retro_cjac_3110
ATGCCCAAGTTTTATTGTGACTACTGCGATACATACCTCACCCATGACTCTCCATCTGTGAGAAAGACACACTGCAGTGG
TAGGAAACACAAAGAGAATGTGAAAGACTACTATCAGAAATGGATGGAAGAGCAGGCTCAGAGCCTGATTGACAAAACAA
CGGCTGCATTTCAACAAGGAAAGATACCTCCTACTCCATTCTCTGCTCCTCCTCCTGCAGGGGCGATGATACCACCTCCC
CCAAGTCTTCCAGGTCCTTCTCACCCTGGTATGATGCCAGTACCCCATATGGGGGGCCCTCCCATGATGCCAATGATGGG
CCCTCTTCTCCTGGGATGATGCCAGTGGGACCTGCTCCTGGAATGAGGCCACCCATGGGAGGCCATATGCCAATGATGCC
TGGGCCCCCAATGATGAGACCTCCTGCCTGTCCCATGATGGTGCCCACTCAGCCTGGAATGACTCGACCACACAGA

Alignment

ORF - retro_cjac_3110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAP
          MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAP
Retrocopy MPKFYCDYCDTYLTHDSPSVRKTHCSGRKHKENVKDYYQKWMEEQAQSLIDKTTAAFQQGKIPPTPFSAP

Parental  PPAGAMIPPPPSLPGPPRPGMMPAPHMGGPPMMPMM-GPPPPGMMPVGPAPGMRPPMGGHMPMMPGPPMM
          PPAGAMIPPPPSLPGP..PGMMP.PHMGGPPMMPMM.GP..PGMMPVGPAPGMRPPMGGHMPMMPGPPMM
Retrocopy PPAGAMIPPPPSLPGPSHPGMMPVPHMGGPPMMPMM<GPSSPGMMPVGPAPGMRPPMGGHMPMMPGPPMM

Parental  RPPARPMMVPTRPGMTRPDR
          RPPA.PMMVPT.PGMTRP.R
Retrocopy RPPACPMMVPTQPGMTRPHR

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	0.07 RPM	8.36 RPM
SRP051959_heart	0.12 RPM	8.61 RPM
SRP051959_kidney	0.09 RPM	8.43 RPM
SRP051959_liver	0.02 RPM	8.53 RPM
SRP051959_lung	0.02 RPM	9.89 RPM
SRP051959_lymph_node	0.09 RPM	8.97 RPM
SRP051959_skeletal_muscle	0.07 RPM	12.51 RPM
SRP051959_spleen	0.15 RPM	9.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3110 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3110 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3110 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 26 parental genes, and 169 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000963	7 retrocopies	retro_amel_1237, retro_amel_1249, retro_amel_149, retro_amel_1522, retro_amel_1523, retro_amel_592, retro_amel_988,
Bos taurus	ENSBTAG00000024549	1 retrocopy	retro_btau_1636,
Canis familiaris	ENSCAFG00000001231	3 retrocopies	retro_cfam_348, retro_cfam_402, retro_cfam_409,
Callithrix jacchus	ENSCJAG00000015321	16 retrocopies	retro_cjac_1009, retro_cjac_1015, retro_cjac_1064, retro_cjac_1750, retro_cjac_1937, retro_cjac_2014, retro_cjac_2395, retro_cjac_2456, retro_cjac_2785, retro_cjac_3056, retro_cjac_3110 , retro_cjac_400, retro_cjac_4010, retro_cjac_617, retro_cjac_770, retro_cjac_873,
Cavia porcellus	ENSCPOG00000008563	3 retrocopies	retro_cpor_1529, retro_cpor_1540, retro_cpor_288,
Felis catus	ENSFCAG00000005876	12 retrocopies	retro_fcat_1008, retro_fcat_1088, retro_fcat_1265, retro_fcat_1545, retro_fcat_1599, retro_fcat_161, retro_fcat_1664, retro_fcat_1814, retro_fcat_446, retro_fcat_578, retro_fcat_627, retro_fcat_922,
Homo sapiens	ENSG00000124562	6 retrocopies	retro_hsap_1531, retro_hsap_1866, retro_hsap_2865, retro_hsap_3195, retro_hsap_3829, retro_hsap_4241,
Gorilla gorilla	ENSGGOG00000012499	7 retrocopies	retro_ggor_1169, retro_ggor_1333, retro_ggor_1364, retro_ggor_1981, retro_ggor_2577, retro_ggor_2699, retro_ggor_2842,
Loxodonta africana	ENSLAFG00000013534	2 retrocopies	retro_lafr_621, retro_lafr_878,
Myotis lucifugus	ENSMLUG00000002488	8 retrocopies	retro_mluc_1246, retro_mluc_1627, retro_mluc_2020, retro_mluc_2099, retro_mluc_2144, retro_mluc_2332, retro_mluc_735, retro_mluc_962,
Macaca mulatta	ENSMMUG00000000869	9 retrocopies	retro_mmul_1148, retro_mmul_1161, retro_mmul_1343, retro_mmul_1465, retro_mmul_1573, retro_mmul_1626, retro_mmul_2016, retro_mmul_2314, retro_mmul_678,
Monodelphis domestica	ENSMODG00000013904	1 retrocopy	retro_mdom_22,
Mustela putorius furo	ENSMPUG00000003210	7 retrocopies	retro_mputfur_1233, retro_mputfur_1260, retro_mputfur_1396, retro_mputfur_374, retro_mputfur_441, retro_mputfur_519, retro_mputfur_531,
Mus musculus	ENSMUSG00000024217	21 retrocopies	retro_mmus_1079, retro_mmus_1084, retro_mmus_1231, retro_mmus_1313, retro_mmus_1374, retro_mmus_1400, retro_mmus_1515, retro_mmus_1649, retro_mmus_1673, retro_mmus_1781, retro_mmus_1876, retro_mmus_2087, retro_mmus_2211, retro_mmus_2506, retro_mmus_2973, retro_mmus_3089, retro_mmus_3366, retro_mmus_431, retro_mmus_531, retro_mmus_566, retro_mmus_638,
Nomascus leucogenys	ENSNLEG00000008392	2 retrocopies	retro_nleu_2129, retro_nleu_99,
Oryctolagus cuniculus	ENSOCUG00000026668	3 retrocopies	retro_ocun_1019, retro_ocun_184, retro_ocun_196,
Otolemur garnettii	ENSOGAG00000008755	9 retrocopies	retro_ogar_1040, retro_ogar_130, retro_ogar_1763, retro_ogar_183, retro_ogar_2434, retro_ogar_3064, retro_ogar_3322, retro_ogar_3377, retro_ogar_697,
Procavia capensis	ENSPCAG00000016885	1 retrocopy	retro_pcap_34,
Pongo abelii	ENSPPYG00000029902	3 retrocopies	retro_pabe_2367, retro_pabe_3397, retro_pabe_3524,
Pan troglodytes	ENSPTRG00000018070	6 retrocopies	retro_ptro_1037, retro_ptro_1283, retro_ptro_1937, retro_ptro_2249, retro_ptro_2606, retro_ptro_2883,
Pteropus vampyrus	ENSPVAG00000015597	1 retrocopy	retro_pvam_1213,
Rattus norvegicus	ENSRNOG00000000493	30 retrocopies	retro_rnor_1027, retro_rnor_1079, retro_rnor_1100, retro_rnor_1196, retro_rnor_1219, retro_rnor_1421, retro_rnor_1628, retro_rnor_1637, retro_rnor_1701, retro_rnor_1761, retro_rnor_2259, retro_rnor_2261, retro_rnor_2385, retro_rnor_2480, retro_rnor_2663, retro_rnor_2875, retro_rnor_2893, retro_rnor_445, retro_rnor_483, retro_rnor_495, retro_rnor_502, retro_rnor_630, retro_rnor_705, retro_rnor_706, retro_rnor_707, retro_rnor_730, retro_rnor_747, retro_rnor_778, retro_rnor_802, retro_rnor_889,
Sarcophilus harrisii	ENSSHAG00000000945	1 retrocopy	retro_shar_112,
Sus scrofa	ENSSSCG00000001531	1 retrocopy	retro_sscr_709,
Ictidomys tridecemlineatus	ENSSTOG00000013786	3 retrocopies	retro_itri_1278, retro_itri_1374, retro_itri_861,
Tarsius syrichta	ENSTSYG00000011216	6 retrocopies	retro_tsyr_1198, retro_tsyr_1475, retro_tsyr_1746, retro_tsyr_185, retro_tsyr_260, retro_tsyr_690,