RetrogeneDB ID: retro_cjac_3470

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: ACFV01180985.1:2173..2691(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000016729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: GCSH
• Ensembl ID: ENSCJAG00000016654
• Aliases: None
• Description: glycine cleavage system protein H (aminomethyl carrier) [Source:HGNC Symbol;Acc:4208]

Sequence

>retro_cjac_3470
ATGGCGCTGCGAGCGGTGCGGAGCGTGCGGGCCGTGCTCTGCACCCTGCGCGCGGTCCCGTCACCCGCCGCGTCCTGCCA
GCCGAGGCCCTGGCAGCTGGGGGCAGGCGCCGTCCGGAAGCTGCGCACAGGACCCGCTCTGCTTTCGATGCGTAAATTCA
CAGAGAAACATGAATGGATAACAACAGAAAATGGTATTGGAACAGTGGGAATCAGCAATTTTGCACAGGAAGCGTTGGGA
GATATTGTTTACTGTAGTCTGCCTGAAGTTGGGACAAAATTGAATAACAAGATGAATTTGGTGCTTTGGAAAGTGTGAAT
GCTGCTAGTGAATTCTATTCTCCTTTATCAGGAGAAGTCACCGAAATTAATGAAGCTCTTGCAGAAAATCCAGGACTTGT
AAACAAATCTTGTTATGAAGATGGTTGGCTGATCAAGATGACACTGAGTAACCCTTCAGAACTAGATGAACTTAAGAGTG
AAGAAGCCTATGAGAAATACATAAAATCTATTGAGGAG

Alignment

ORF - retro_cjac_3470 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.83 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MALRAARSVRAVLCTLRAVPSPAASCPPRPWQLGAGAVRKLRTGPALLSVRKFTEKHEWITTENGIGTVG
          MALRA.RSVRAVLCTLRAVPSPAASC.PRPWQLGAGAVRKLRTGPALLS.RKFTEKHEWITTENGIGTVG
Retrocopy MALRAVRSVRAVLCTLRAVPSPAASCQPRPWQLGAGAVRKLRTGPALLSMRKFTEKHEWITTENGIGTVG

Parental  ISNFAQEALGDVVYCSLPEVGTKLNK-QDEFGALESVKAASELYSPLSGEVTEINEALAENPGLVNKSCY
          ISNFAQEALGD.VYCSLPEVGTKLN..QDEFGALESV.AASE.YSPLSGEVTEINEALAENPGLVNKSCY
Retrocopy ISNFAQEALGDIVYCSLPEVGTKLNN<QDEFGALESVNAASEFYSPLSGEVTEINEALAENPGLVNKSCY

Parental  EDGWLIKMTLSNPSELDELMSEEAYEKYIKSIEE
          EDGWLIKMTLSNPSELDEL.SEEAYEKYIKSIEE
Retrocopy EDGWLIKMTLSNPSELDELKSEEAYEKYIKSIEE

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	3.39 RPM
SRP051959_heart	0.05 RPM	7.47 RPM
SRP051959_kidney	0.07 RPM	11.83 RPM
SRP051959_liver	0.04 RPM	34.98 RPM
SRP051959_lung	0.02 RPM	1.92 RPM
SRP051959_lymph_node	0.02 RPM	1.42 RPM
SRP051959_skeletal_muscle	0.04 RPM	6.66 RPM
SRP051959_spleen	0.00 RPM	1.83 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3470 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3470 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3470 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 110 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000008905	1 retrocopy	retro_acar_75,
Ailuropoda melanoleuca	ENSAMEG00000013959	5 retrocopies	retro_amel_1362, retro_amel_1877, retro_amel_229, retro_amel_432, retro_amel_80,
Bos taurus	ENSBTAG00000006795	8 retrocopies	retro_btau_1128, retro_btau_12, retro_btau_1483, retro_btau_1543, retro_btau_1628, retro_btau_246, retro_btau_265, retro_btau_94,
Canis familiaris	ENSCAFG00000020014	5 retrocopies	retro_cfam_1249, retro_cfam_1543, retro_cfam_358, retro_cfam_618, retro_cfam_732,
Choloepus hoffmanni	ENSCHOG00000002434	37 retrocopies	retro_chof_1011, retro_chof_1019, retro_chof_1123, retro_chof_1213, retro_chof_1324, retro_chof_1410, retro_chof_1482, retro_chof_1550, retro_chof_163, retro_chof_1647, retro_chof_1659, retro_chof_1690, retro_chof_1705, retro_chof_1722, retro_chof_178, retro_chof_1781, retro_chof_1787, retro_chof_219, retro_chof_2264, retro_chof_2289, retro_chof_2319, retro_chof_2412, retro_chof_2466, retro_chof_2494, retro_chof_2632, retro_chof_2657, retro_chof_283, retro_chof_335, retro_chof_361, retro_chof_362, retro_chof_363, retro_chof_419, retro_chof_433, retro_chof_477, retro_chof_597, retro_chof_755, retro_chof_931,
Callithrix jacchus	ENSCJAG00000016654	8 retrocopies	retro_cjac_1071, retro_cjac_1576, retro_cjac_1674, retro_cjac_1804, retro_cjac_2650, retro_cjac_3280, retro_cjac_3470 , retro_cjac_552,
Felis catus	ENSFCAG00000013038	8 retrocopies	retro_fcat_1007, retro_fcat_1112, retro_fcat_1294, retro_fcat_1435, retro_fcat_1627, retro_fcat_1920, retro_fcat_215, retro_fcat_354,
Loxodonta africana	ENSLAFG00000015586	3 retrocopies	retro_lafr_554, retro_lafr_822, retro_lafr_900,
Myotis lucifugus	ENSMLUG00000005783	12 retrocopies	retro_mluc_1151, retro_mluc_1221, retro_mluc_1466, retro_mluc_1538, retro_mluc_1659, retro_mluc_1685, retro_mluc_2089, retro_mluc_2090, retro_mluc_2139, retro_mluc_2314, retro_mluc_2411, retro_mluc_709,
Macaca mulatta	ENSMMUG00000013088	5 retrocopies	retro_mmul_1192, retro_mmul_2202, retro_mmul_661, retro_mmul_840, retro_mmul_960,
Mustela putorius furo	ENSMPUG00000009677	4 retrocopies	retro_mputfur_1434, retro_mputfur_1492, retro_mputfur_349, retro_mputfur_809,
Nomascus leucogenys	ENSNLEG00000026844	1 retrocopy	retro_nleu_365,
Ochotona princeps	ENSOPRG00000003281	1 retrocopy	retro_opri_790,
Procavia capensis	ENSPCAG00000005820	1 retrocopy	retro_pcap_207,
Pteropus vampyrus	ENSPVAG00000009956	8 retrocopies	retro_pvam_1253, retro_pvam_1474, retro_pvam_1481, retro_pvam_194, retro_pvam_552, retro_pvam_583, retro_pvam_78, retro_pvam_958,
Sarcophilus harrisii	ENSSHAG00000005529	1 retrocopy	retro_shar_239,
Ictidomys tridecemlineatus	ENSSTOG00000016433	2 retrocopies	retro_itri_31, retro_itri_34,