RetrogeneDB ID: retro_cjac_2927

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 7:106268108..106268961(+)
• 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_2927
CGAAGAACAACTGATTTTTCTGATTTCTTAAGCATTGTAGGCTGTACGGAAGGTAGACATAATAGTGAGAAGCCACCTGA
GCCAGTCAAACCTGAAGTCAAGGCTACTGAGAAGAAGGAACTATCTGAATTGAAACCCAAATTTCAGGAATACATCATTC
AAGCCCCTGAGCCAGTAGAAGCAATAAAAAGGCCAAGCCCACATGAACCAATGACAAATTGGGAATTAAAAGTATCTGCC
TCCCTAAAATAAGCACTTGATAAACTGTCATCAGGGAATGAAGAAGATAAGGAAGAAGAAGACAATGTTGAAATTAAGAT
TGGGACCTCAGGTGAAAACGGAGGGTGTTCAAAGACATTGGTGTTTCGAGAATCTAGAAGAAGTCTGTATGTCATTCTGT
AGAACCTATTTTTTTAATGAGGGGATGAAATACTAGAGCTGTTGTCGAAGAAAAACTTCTGATTTTAATACATTCTTAGC
CCAAGAGTGCTGTCAACAGGGAAACACATGTTGACTAAAAAGGATGCTGGGAAAAAATTGTTCCATGTAGACATGACGGG
CATCAGACTGGAGGTGGAGTTACCATTTCAGTATATGCTAAAAATTCACTTCCAGAACTTAGTCGACTAGAAGCAGATAG
CACATTGTTAAATGTGAGCCTGTATTTGAAGGAGAGAAGCAATTCGATCAAAATGTGCAATTATGGGGTGTGATTGATGT
AAACCGAAGTTATGTAACTATGACTGCAGCAAAGATTGAGGTCACTGTGAGAAAAGCTGATCCAATGCAGTGGGCCAGTC
TTGAAGTGACTGCAGTGAAAAAGCAGGAAAAACAAAAAGGCGGCACAACAGAT

Alignment

ORF - retro_cjac_2927 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.74 %
• Parental protein coverage: 86.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRTTDFSDFLSIVGCTKGRHNSEKPPEPVKPEVKTTEKKELSDLKPKFREHIIQAPKPVEAIKRPSPDEP
          RRTTDFSDFLSIVGCT.GRHNSEKPPEPVKPEVK.TEKKELS.LKPKF.E.IIQAP.PVEAIKRPSP.EP
Retrocopy RRTTDFSDFLSIVGCTEGRHNSEKPPEPVKPEVKATEKKELSELKPKFQEYIIQAPEPVEAIKRPSPHEP

Parental  MTNLELKISASLKQALDKLKLSSGNEEDKKEEDNDEIKI-GTSCKNGGCSKTYRGLESLEEVCVYHSGVP
          MTN.ELK.SASLK.ALDKL..SSGNEEDK.EEDN.EIKI.G...K..G........E.LEEVC.......
Retrocopy MTNWELKVSASLK*ALDKL--SSGNEEDKEEEDNVEIKI>GPQVKTEGVQRHWC-FENLEEVCMSFCRTY

Parental  IFHEGMKYWSCCRRKTSDFNTFLAQEGC-TTGKHMWTKKDAGKK-VVPCRHDWHQTGGEVTISVYAKNSL
          .F.EGMKY.SCCRRKTSDFNTFLAQE.C..TGKHM.TKKDAGKK..VPCRHD.HQTGG.VTISVYAKNSL
Retrocopy FFNEGMKY*SCCRRKTSDFNTFLAQECC<STGKHMLTKKDAGKK<IVPCRHDGHQTGGGVTISVYAKNSL

Parental  PELSRVEANSTLVNVHI-VFEGEKEFDQNVKLWGVIDVKRSYVTMTATKIEITMRKAEPMQWASLELPAA
          PELSR.EA.STL.NV...VFEGEK.FDQNV.LWGVIDV.RSYVTMTA.KIE.T.RKA.PMQWASLE..A.
Retrocopy PELSRLEADSTLLNVSL<VFEGEKQFDQNVQLWGVIDVNRSYVTMTAAKIEVTVRKADPMQWASLEVTAV

Parental  KKQEKQKDDTTD
          KKQEKQK..TTD
Retrocopy KKQEKQKGGTTD

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

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2927 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2927 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2927 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_461

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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,