RetrogeneDB ID: retro_cjac_2045

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:29783575..29784516(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPDH1
• Ensembl ID: ENSCJAG00000017770
• Aliases: None
• Description: Inosine-5'-monophosphate dehydrogenase A [Source:UniProtKB/TrEMBL;Acc:F7EBY6]

Sequence

>retro_cjac_2045
GCAAATGAGATCGTGTAGCCTAGCAAGAAAGGGAAGCCTGTTGTCAATGATCGTGATGAGCTGGTGACCATCACTGTCCG
CACCCACCTGAAGAAGCACCGAGATTACCCTCTGGCCTCCAAGGATTCCCACTAACAGCTACTGTGTGGGGCAGCTGTGG
GCAACCGTGAGGATGACAAATACTGCCTGCACCTGCTCACCCAGGTGGGCATCCACGTCATGGTCTTGGACTCATCCCAA
CAGAACTCGGTGTATGAGATCGCCACAATGCATTACGTCAAACAGAAGTACCACCACCTGCAGGTGATTGCTGGGAATGT
GGTGACAGCAGCCTAGGCCGAGAACCTGACTGACGCTGGTGAGGACGCGCTGCACGTGGGCTTGGGCTGCGGCTCCATCT
GCATCACCCAGGAAGTGATTGCCTGCAGTAAGCCCCAGGGCACTGCTGTGTACAAGGTGGCTGAGTATGCCCGGGGCTTT
GGTGTGCCTATCATAGCCGATTGCGGCATCTAGATCATGGGATATGTGGTCCAGGCCCTGGGCCCTTGGAGCTTCCACAG
TGATGATGGGCTCACTGCTGGCCGCCCCCACGGAGGCCCCCAGCCAGTACTCAGACAGGGTGCGACTCAAGAAGTACCAG
GGAATGGGCTTGGCTGCCAGGGAGAAGAGCAGCAGCAGCCAGAAACGATACTTCAGAGAGGGGGATAAGGTAAAGATCTC
GCACGGTGTCTTGGGCTCCATCCAGGACAAAGGGTCCATTCAGAAGTTCGTGTCCTACCTCACAGCGGGCATCCAGCACG
GCTGCCAGGATATCGGGGCCACAGCCTGTATGTCCTTCAGTCCCTGACGTACTCAGGAGAGCTCAAGTTTGAGAAGCGAC
CATGTCGGCCCAGATCAAGGATGGCGTCCGTGACCTGCAATCTTAAGAGAGAAGTGGCTAC

Alignment

ORF - retro_cjac_2045 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.32 %
• Parental protein coverage: 53.99 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ANEILQRSKKGKLPIVNDHDELVAIIARTDLKKNRDYPLASKDSHKQLLCGAAVGTREDDKYRLDLLTQA
          ANEI...SKKGK.P.VND.DELV.I..RT.LKK.RDYPLASKDSH.QLLCGAAVG.REDDKY.L.LLTQ.
Retrocopy ANEIV*PSKKGK-PVVNDRDELVTITVRTHLKKHRDYPLASKDSH*QLLCGAAVGNREDDKYCLHLLTQV

Parental  GVDVIVLDSSQGNSVYQIAMVHYIKQKYPHLQVIGGNVVTAAQAKNLIDAGVDGLRVGMGCGSICITQEV
          G..V.VLDSSQ.NSVY.IA..HY.KQKY.HLQVI.GNVVTAA.A.NL.DAG.D.L.VG.GCGSICITQEV
Retrocopy GIHVMVLDSSQQNSVYEIATMHYVKQKYHHLQVIAGNVVTAA*AENLTDAGEDALHVGLGCGSICITQEV

Parental  MACGRPQGTAVYKVAEYARRFGVPIIADGGIQTVGHVVKAL-ALGASTVMMGSLLAATTEAPGEYFFSDG
          .AC..PQGTAVYKVAEYAR.FGVPIIAD.GI...G.VV.AL.ALGASTVMMGSLLAA.TEAP..Y..SD.
Retrocopy IACSKPQGTAVYKVAEYARGFGVPIIADCGI*IMGYVVQAL>ALGASTVMMGSLLAAPTEAPSQY--SDR

Parental  VRLKKYRGMGSLDAMEKSSSSQKRYFSEGDKVKIAQGVSGSIQDKGSIQKFVPYLIAGIQHGCQDIGA-R
          VRLKKY.GMG.L.A.EKSSSSQKRYF.EGDKVKI..GV.GSIQDKGSIQKFV.YL.AGIQHGCQDIGA..
Retrocopy VRLKKYQGMG-LAAREKSSSSQKRYFREGDKVKISHGVLGSIQDKGSIQKFVSYLTAGIQHGCQDIGA<H

Parental  SLSVLRSMMYSGELKFEKR-TMSAQIEGGVHGLHSYEKRLY
          SL.VL.S..YSGELKFEKR.TMSAQI..GV..L.S.E...Y
Retrocopy SLYVLQSLTYSGELKFEKR<TMSAQIKDGVRDLQS*ERSGY

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	3.97 RPM
SRP051959_heart	0.02 RPM	4.51 RPM
SRP051959_kidney	0.00 RPM	2.73 RPM
SRP051959_liver	0.00 RPM	3.10 RPM
SRP051959_lung	0.00 RPM	4.21 RPM
SRP051959_lymph_node	0.00 RPM	4.20 RPM
SRP051959_skeletal_muscle	0.00 RPM	2.07 RPM
SRP051959_spleen	0.00 RPM	4.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2045 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2045 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2045 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017770	1 retrocopy	retro_cjac_2045 ,
Homo sapiens	ENSG00000106348	7 retrocopies	retro_hsap_2360, retro_hsap_2368, retro_hsap_2608, retro_hsap_3797, retro_hsap_4005, retro_hsap_4247, retro_hsap_4808,
Gorilla gorilla	ENSGGOG00000003963	6 retrocopies	retro_ggor_1790, retro_ggor_1798, retro_ggor_1827, retro_ggor_2551, retro_ggor_2688, retro_ggor_2993,
Macropus eugenii	ENSMEUG00000016082	2 retrocopies	retro_meug_2095, retro_meug_542,
Macaca mulatta	ENSMMUG00000014509	2 retrocopies	retro_mmul_1551, retro_mmul_317,
Nomascus leucogenys	ENSNLEG00000012341	1 retrocopy	retro_nleu_2508,
Pongo abelii	ENSPPYG00000017976	7 retrocopies	retro_pabe_2133, retro_pabe_2138, retro_pabe_2346, retro_pabe_3102, retro_pabe_3292, retro_pabe_3392, retro_pabe_3736,
Pan troglodytes	ENSPTRG00000019660	7 retrocopies	retro_ptro_1087, retro_ptro_1724, retro_ptro_1758, retro_ptro_2575, retro_ptro_2719, retro_ptro_2886, retro_ptro_3198,