RetrogeneDB ID: retro_cjac_815

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 10:115309576..115310565(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSCJAG00000000903
• Aliases: None
• Description: None

Sequence

>retro_cjac_815
GCCTTGTTGTGCTACAATCGGGGCTGCGGCAAGTGCTTCGATCCTGAGACCAATTCCAATGATGCTTGCACATACCGCCC
AGGTGTTCCTGTCTTTTACAATGCATTAAACGGTTGGTCTTGCTGTAAGAGAAGAACAACTGATTTTTCTGATTTCTTAG
CATTGTAGGCTCTGCAAAAGGTAGACATAATAGTGAGAAGCCACCTGAGCCTGTCAAACCTGAAGTCAAGACCACCACGA
AGAAGAAACTATCTGAATTGAAACCCAAATTTCAGGAACACATTCAAGCCCCTAAGCCAGTAGAAGCAATAAAAAGGCCA
AGTCTGGATGAACTAATGGCAAATTTGGATATAAAAATATCTGCCTCCCTAAAACAAGCACTTGATAAACTTAAACTGTT
ATCAGGGAATGAAGAAAATAGGAAAGAAGAAGGTAGTGATGAAATTAAGATTGGGACCTCGTGTAAGAATGGAGGGTGTT
CAAAGACATATCGGGCTCTAGAGAGTCTAGAAGTCTGTGTGTATCACCCTGGAGTACCTGTTTTCCATGAAGGGGTGAAA
TACCGGAGCTGTTGTAGAAGAAAAACAAACATCTAATTTTAATACATTCTTAGCCCAAGAGGACTGGACAACAGAAAAAC
ACACGTGGACTGAAAAGGATGCCGGGAAAAATGTCGTTCCCTGTAGATATGACTGGCATCAGACTGGAGGTGAAGTCATC
ACTTCAGTATATGCTAAAAATTCACTTCCAGAACTTAGTCAAGTAGAAGCAAATGGCGCGTTGTTAAATGTGTGCATTGT
ATTGGAAGGAAAGAAGGAATTTGATCAAAATGTGAAATTATGGGGTGTGACTGATTTAAAGCAAAGTTAATAACTGTGAC
TGCAACAAAGACTAACATCACTATGAGAAAAGCTGAACCGATTCAGTAGACAAGACTTGAACTGGCTGCAGCCAAAGAGC
AGGAAAAACAAAAAGGCGACACAACAGAT

Alignment

ORF - retro_cjac_815 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.81 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SLLCYNRGCGQRFDPETNSDEACTYHPGVPVFHDALKGWSCCKRRTTDFSDFL-SIVGCTKGRHNSEKPP
          .LLCYNRGCG..FDPETNS..ACTY.PGVPVF..AL.GWSCCKRRTTDFSDFL.SIVG..KGRHNSEKPP
Retrocopy ALLCYNRGCGKCFDPETNSNDACTYRPGVPVFYNALNGWSCCKRRTTDFSDFL<SIVGSAKGRHNSEKPP

Parental  EPVKPEVKTTEKKELSDLKPKFREHIIQAPKPVEAIKRPSPDEPMTNLELKISASLKQALDKLKLSSGNE
          EPVKPEVKTT.KK.LS.LKPKF.EHI.QAPKPVEAIKRPS.DE.M.NL..KISASLKQALDKLKL.SGNE
Retrocopy EPVKPEVKTTTKKKLSELKPKFQEHI-QAPKPVEAIKRPSLDELMANLDIKISASLKQALDKLKLLSGNE

Parental  EDKKEEDNDEIKIGTSCKNGGCSKTYRGLESLEEVCVYHSGVPIFHEGMKYWS-CCRR-KTSDFNTFLAQ
          E..KEE..DEIKIGTSCKNGGCSKTYR.LESLE.VCVYH.GVP.FHEG.KY.S.C.R...TS.FNTFLAQ
Retrocopy ENRKEEGSDEIKIGTSCKNGGCSKTYRALESLE-VCVYHPGVPVFHEGVKYRSCCRRK>QTSNFNTFLAQ

Parental  EGCTTGKHMWTKKDAGKKVVPCRHDWHQTGGEVTISVYAKNSLPELSRVEANSTLVNVHIVFEGEKEFDQ
          E..TT.KH.WT.KDAGK.VVPCR.DWHQTGGEV..SVYAKNSLPELS.VEAN..L.NV.IV.EG.KEFDQ
Retrocopy EDWTTEKHTWTEKDAGKNVVPCRYDWHQTGGEVITSVYAKNSLPELSQVEANGALLNVCIVLEGKKEFDQ

Parental  NVKLWGVIDVKRS-YVTMTATKIEITMRKAEPMQWASLELPAAKKQEKQKDDTTD
          NVKLWGV.D.K.S...T.TATK..ITMRKAEP.Q...LEL.AAK.QEKQK.DTTD
Retrocopy NVKLWGVTDLKQS<LITVTATKTNITMRKAEPIQ*TRLELAAAKEQEKQKGDTTD

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	28.36 RPM
SRP051959_heart	0.04 RPM	24.08 RPM
SRP051959_kidney	0.00 RPM	26.71 RPM
SRP051959_liver	0.02 RPM	35.61 RPM
SRP051959_lung	0.02 RPM	57.20 RPM
SRP051959_lymph_node	0.00 RPM	79.59 RPM
SRP051959_skeletal_muscle	0.02 RPM	20.59 RPM
SRP051959_spleen	0.06 RPM	56.51 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_815 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_815 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_815 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1452
Pan troglodytes	retro_ptro_988
Gorilla gorilla	retro_ggor_1117
Pongo abelii	retro_pabe_1199

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000903	4 retrocopies	retro_cjac_2220, retro_cjac_2927, retro_cjac_4147, retro_cjac_815 ,
Echinops telfairi	ENSETEG00000013104	2 retrocopies	retro_etel_1713, retro_etel_1860,
Felis catus	ENSFCAG00000019389	1 retrocopy	retro_fcat_137,
Homo sapiens	ENSG00000110172	3 retrocopies	retro_hsap_1452, retro_hsap_1903, retro_hsap_2252,
Gorilla gorilla	ENSGGOG00000027396	3 retrocopies	retro_ggor_1117, retro_ggor_1118, retro_ggor_1679,
Loxodonta africana	ENSLAFG00000017340	1 retrocopy	retro_lafr_401,
Macaca mulatta	ENSMMUG00000005209	2 retrocopies	retro_mmul_1024, retro_mmul_1923,
Nomascus leucogenys	ENSNLEG00000007079	5 retrocopies	retro_nleu_1085, retro_nleu_1232, retro_nleu_1320, retro_nleu_752, retro_nleu_981,
Oryctolagus cuniculus	ENSOCUG00000014147	1 retrocopy	retro_ocun_1595,
Otolemur garnettii	ENSOGAG00000003523	1 retrocopy	retro_ogar_2724,
Pongo abelii	ENSPPYG00000003764	5 retrocopies	retro_pabe_1199, retro_pabe_1554, retro_pabe_1734, retro_pabe_1959, retro_pabe_461,
Pan troglodytes	ENSPTRG00000004164	3 retrocopies	retro_ptro_1253, retro_ptro_1595, retro_ptro_988,
Tupaia belangeri	ENSTBEG00000002910	1 retrocopy	retro_tbel_2891,
Tarsius syrichta	ENSTSYG00000004205	1 retrocopy	retro_tsyr_1581,