RetrogeneDB ID: retro_cjac_1709

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 19:34665536..34667048(+)
• Located in intron of: ENSCJAG00000016856

Retrocopy information

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

Parental gene information

• Parental gene symbol: UGP2
• Ensembl ID: ENSCJAG00000006960
• Aliases: None
• Description: None

Sequence

>retro_cjac_1709
GAAGATCTTAGCAAAGCAATGTCTCAAGATGGCACTTCTCAGTTCCAAGAAGTCATTCGGCAAGAGCTAGATTTATCTAT
GAAGAAGGAACTAGAAAACATACTCACCACAGCATCCTCACATGAGTTTGAGCACACTAGAAAAGACCTGGATGGATTTT
GGAAGCTATTTCATTGATTTTTGCAAGAAAAGGGGCCTTCTGTGGATTGGGGAAAAATTCAGAGACCTCCAGAAGATTCT
ATTCAACCCTATGAAAAGATAAAGGCCAGGGGCTTGCCTGATATATATCTTCTGTGTTGAACAAACTAGTGGTGGTGAAA
CTCAGTGGTGGTTTGGGAACCAGCATGGGCTGCAAAGGCCCTAAAAGTCTTATTGGTGTGAGGAATGAGAATACCTTTCT
GGATCTGACTGTTCAGCAAATCGAACATTTGAATAAAACCTACAATACAGATGTTCTCCTTGTTTTAATGAACTATTTTA
ACACAGATGAAGATACCAAAAAAATACTACAGAAGTACAGTCATTGTTGTGTGAAAATCTACACTTTTAATAAAAGCAGG
TACCCGAGGATTAATAAGGAATCTTTACTTCCTGTAGCAAAGAATGTGTCTTACTCAGGGGAAAATACAGAAGCTTGGTA
CCCTCCAGGTCATGGTGATATTTACGCCAGTTTCTACAACTCTGGTTAGCTTGATACCTTTATAGGAGAAGGCAAAGAGT
ATATTTTTGTGTCTAACTTAGATAATCTCGGTGCCACAGTGGATCTGTATATTCTTAATCATCTAATGAACCCACCCAAT
GGAAAATGCTGTGAATTTGTCATGGAAGTCACAAATAAAACACGTGCAGATGTAAAGGGTGGGACACTCACTCAATATGA
AGGCAAACTGAGACTGGTGGAAATTGCTCAAGTGCCAAAAGCACATGTTGATGAGTTCAAGTCTGTGTCAAAGTTCAAAA
TATTTAACATAAACAACCTATGGATTTCTCCTGCAGCAGTTAAAAGACTGCAGGAGCAGAATGCCATTGACGTGGAAATC
ATTGTGAATGCAAAGACTTTGGATGGAGGCCTGAATGTCATTCAGTTAGAAACTGCAGTAGGGGCTGCCATCGAACGTTT
TGAGAATTCTCTAGGTATTAATGTGCCAAGGAGCCATTTTCTGCCTGTCAAAACCACATCAGATCTCTTGCTGGTGATGT
CAAACCTCTATAGCCTTAATGCAGGATCTCTGACAATGAGTGATAAGCGGGAATTTCCTACAATGCCCTTGGTTAAATTA
GGCAGTTCTTTTACAAAGTTTCAAGATTATCTAAGAAGATTTGAAAGTATACCAGATATTCTTGAATTGGATCACCTCAC
AGTTTCAGGAGATGTGACATTTGGAAAGAATGTTTCATTAAAGGGAGGGAACTGTTATCATTATTGCAAATCATGGTGGC
AGAATTGACATCCCACCTGGAGCAGTATTCGAGAACCAGATTGTATCTGGGAACCTTCACATCTTGGACCAC

Alignment

ORF - retro_cjac_1709 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QDLSKAMSQDGASQFQEVIRQELELSVKKELEKILTTASSHEFEHTKKDLDGFRKLFHRFLQEKGPSVDW
          .DLSKAMSQDG.SQFQEVIRQEL.LS.KKELE.ILTTASSHEFEHT.KDLDGF.KLFH.FLQEKGPSVDW
Retrocopy EDLSKAMSQDGTSQFQEVIRQELDLSMKKELENILTTASSHEFEHTRKDLDGFWKLFH*FLQEKGPSVDW

Parental  GKIQRPPEDSIQPYEKIKARGLPD-NISSVLNKLVVVKLNGGLGTSMGCKGPKSLIGVRNENTFLDLTVQ
          GKIQRPPEDSIQPYEKIKARGLPD..ISSVLNKLVVVKL.GGLGTSMGCKGPKSLIGVRNENTFLDLTVQ
Retrocopy GKIQRPPEDSIQPYEKIKARGLPD<YISSVLNKLVVVKLSGGLGTSMGCKGPKSLIGVRNENTFLDLTVQ

Parental  QIEHLNKTYNTDVPLVLMNSFNTDEDTKKILQKYNHCRVKIYTFNQSRYPRINKESLLPVAKDVSYSGEN
          QIEHLNKTYNTDV.LVLMN.FNTDEDTKKILQKY.HC.VKIYTFN.SRYPRINKESLLPVAK.VSYSGEN
Retrocopy QIEHLNKTYNTDVLLVLMNYFNTDEDTKKILQKYSHCCVKIYTFNKSRYPRINKESLLPVAKNVSYSGEN

Parental  TEAWYPPGHGDIYASFYNSGLLDTFIGEGKEYIFVSNIDNLGATVDLYILNHLMNPPNGKRCEFVMEVTN
          TEAWYPPGHGDIYASFYNSG.LDTFIGEGKEYIFVSN.DNLGATVDLYILNHLMNPPNGK.CEFVMEVTN
Retrocopy TEAWYPPGHGDIYASFYNSG*LDTFIGEGKEYIFVSNLDNLGATVDLYILNHLMNPPNGKCCEFVMEVTN

Parental  KTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFNTNNLWISLGAVKRLQEQNAIDMEIIV
          KTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFN.NNLWIS..AVKRLQEQNAID.EIIV
Retrocopy KTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFNINNLWISPAAVKRLQEQNAIDVEIIV

Parental  NAKTLDGGLNVIQLETAVGAAIKSFENSLGINVPRSRFLPVKTTSDLLLVMSNLYSLNAGSLTMSEKREF
          NAKTLDGGLNVIQLETAVGAAI..FENSLGINVPRS.FLPVKTTSDLLLVMSNLYSLNAGSLTMS.KREF
Retrocopy NAKTLDGGLNVIQLETAVGAAIERFENSLGINVPRSHFLPVKTTSDLLLVMSNLYSLNAGSLTMSDKREF

Parental  PTVPLVKLGSSFTKVQDYLRRFESIPDMLELDHLTVSGDVTFGKNVSLKG-TVIII-ANHGDRIDIPPGA
          PT.PLVKLGSSFTK.QDYLRRFESIPD.LELDHLTVSGDVTFGKNVSLKG....II.ANHG.RIDIPPGA
Retrocopy PTMPLVKLGSSFTKFQDYLRRFESIPDILELDHLTVSGDVTFGKNVSLKG>GTVIIIANHGGRIDIPPGA

Parental  VLENKIVSGNLRILDH
          V.EN.IVSGNL.ILDH
Retrocopy VFENQIVSGNLHILDH

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	1.51 RPM	57.09 RPM
SRP051959_heart	1.26 RPM	85.37 RPM
SRP051959_kidney	1.35 RPM	36.54 RPM
SRP051959_liver	1.49 RPM	394.68 RPM
SRP051959_lung	1.97 RPM	36.49 RPM
SRP051959_lymph_node	2.63 RPM	32.01 RPM
SRP051959_skeletal_muscle	1.48 RPM	347.75 RPM
SRP051959_spleen	2.75 RPM	36.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1709 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1709 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1709 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006960	1 retrocopy	retro_cjac_1709 ,
Cavia porcellus	ENSCPOG00000008459	1 retrocopy	retro_cpor_811,
Microcebus murinus	ENSMICG00000006509	1 retrocopy	retro_mmur_1277,
Oryctolagus cuniculus	ENSOCUG00000002137	1 retrocopy	retro_ocun_815,
Tursiops truncatus	ENSTTRG00000000694	1 retrocopy	retro_ttru_56,