RetrogeneDB ID: retro_cjac_4166

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:53070675..53071654(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD11
• Ensembl ID: ENSCJAG00000014450
• Aliases: None
• Description: None

Sequence

>retro_cjac_4166
GATCTGTTTCTTGATATGGAAGCAGCTACAGGGCAGGAGGTAGAGCTGTGTTTAGAGTACATCGAATGGGCCAAATCAGA
GAAAATAACTTTCTTACGCCAAACTTTGAAGGCAAGACTGGTGTCTTTGTAATTTGATACCAAGAAGTACCAGGAACCAT
TGCACTTGGGTTCTCAGCTGCTGTGGGAATTGAAAAGATGGACGACAAAGCCCTTCTGGTGGAAGTATAGCTTTCAGAAA
GCAAAACTACCATGCCTTGAGCAACCTGCCGAAAGCCCTAGCTGCCTTAACTCTGCTTGAACCACAGCAAATGCCATCTA
CTGCCCCCCTAAATTGCAGGCCACCTTGGACATGCAGTCATGTATTATCCATGCAGCAGAAGAGAAGGACTGGAGAACTG
CGTACTCATACCTCTACGAGGCATTTGAGGTTTATGACTCCATCGACAGCCCCAAGACCATCATATCACTGAAGAACATG
TTGCTGTGCAAAATCATGCTCAACACCCCAGAAGATGTCCAGACTTTGATGAGCAGGAAGCTTGCACTTCGGTATGCAGG
GAAGCAGACAGAAGCATTAAAATGTGGACTCAGGCTAGCAAGAACAGATAACTGCCAGATTTTGAAAAGGCTCTGACAGA
TTACTGGGCAGAGCTCCAGGATGACCCAATCATCAGCACACACTTGGCAGGGTTGTATAACTTACTGGAACAGAATCTGA
TCCAAGTCATTGAGACTTTTTCTAGAGTACAGATTGAACACATATCTAGTCTCATCAAACTGTCCAAGCCCGATGTGGAA
AGGAAATTATTACAGATGATTCTTGACAAGAAATTTCATTAGATTTTGGACCAGGGGTAAGGTGTCCTGATTATTTTCAG
TGAACCCCCAGGAATAAAACTTATGAAGCTGCTCTGGAAAGAATTCAGAACATGAATAAAGTAGTAGATTCCCTCTACAA
CAAAGCCAAGAAACTGACA

Alignment

ORF - retro_cjac_4166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.93 %
• Parental protein coverage: 77.96 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  DLFLDMEAATGQEVELCLECIEWAKSEKRTFLRQALEARLVSLYFDTKRYQEALHLGSQLLRELK-KMDD
          DLFLDMEAATGQEVELCLE.IEWAKSEK.TFLRQ.L.ARLVSL.FDTK.YQE.LHLGSQLL.ELK.KMDD
Retrocopy DLFLDMEAATGQEVELCLEYIEWAKSEKITFLRQTLKARLVSL*FDTKKYQEPLHLGSQLLWELK<KMDD

Parental  KALLVEVQLLESKT-YHALSNLPKARAALT-SARTTANAIYCPPKLQATLDMQSGIIHAAEEKDWKTAYS
          KALLVEV.L.ESKT.YHALSNLPKA.AALT.SA.TTANAIYCPPKLQATLDMQS.IIHAAEEKDW.TAYS
Retrocopy KALLVEV*LSESKT<YHALSNLPKALAALT<SA*TTANAIYCPPKLQATLDMQSCIIHAAEEKDWRTAYS

Parental  YFYEAFEGYDSIDSPKAITSLKYMLLCKIMLNTPEDVQALVSGKLALRYAGRQTEALKC-VAQASKNRSL
          Y.YEAFE.YDSIDSPK.I.SLK.MLLCKIMLNTPEDVQ.L.S.KLALRYAG.QTEALKC...QASKNR.L
Retrocopy YLYEAFEVYDSIDSPKTIISLKNMLLCKIMLNTPEDVQTLMSRKLALRYAGKQTEALKC<WTQASKNR*L

Parental  ADFEKALTDYRAELRDDPIISTHLAKLYDNLLEQNLIRVIEPFSRVQIEHISSLIKLSKADVERKLSQMI
          .DFEKALTDY.AEL.DDPIISTHLA.LY.NLLEQNLI.VIE.FSRVQIEHISSLIKLSK.DVERKL.QMI
Retrocopy PDFEKALTDYWAELQDDPIISTHLAGLY-NLLEQNLIQVIETFSRVQIEHISSLIKLSKPDVERKLLQMI

Parental  LDKKFHGILDQGEGVLIIFDEP-PVDKTYEAALETIQNMSKVVDSLYNKAKKLT
          LDKKFH.ILDQG.GVLIIF.EP.P..KTYEAALE.IQNM.KVVDSLYNKAKKLT
Retrocopy LDKKFH*ILDQG*GVLIIFSEP<PRNKTYEAALERIQNMNKVVDSLYNKAKKLT

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	13.80 RPM
SRP051959_heart	0.00 RPM	15.84 RPM
SRP051959_kidney	0.00 RPM	16.17 RPM
SRP051959_liver	0.00 RPM	17.13 RPM
SRP051959_lung	0.00 RPM	11.09 RPM
SRP051959_lymph_node	0.00 RPM	14.66 RPM
SRP051959_skeletal_muscle	0.00 RPM	35.90 RPM
SRP051959_spleen	0.00 RPM	14.33 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4166 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4166 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001585	2 retrocopies	retro_cjac_3105, retro_cjac_3117,
Callithrix jacchus	ENSCJAG00000014450	1 retrocopy	retro_cjac_4166 ,
Mus musculus	ENSMUSG00000017428	1 retrocopy	retro_mmus_1973,
Tupaia belangeri	ENSTBEG00000001962	1 retrocopy	retro_tbel_1610,