RetrogeneDB ID: retro_cjac_1164

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:74316988..74317745(-)
• Located in intron of: ENSCJAG00000021104

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000011445
• Aliases: None
• Description: None

Sequence

>retro_cjac_1164
TATTCTATATGTCCATGGCATCTTTATATAAAATACAGCTCATGTTCCACCATACTGCTAGATAACAGTACGGTCAGCAA
GCCTGATCTTAGCCACATGTTAGAAAATGTGACTTTGGCAATATATTACAACATAAAGCACAGATATGCAAACAGATCTC
TGGTTATTTTTGATGAGCCAATACATCTACTTTCACAAGAAAAGACTCCAGGGAAATCCTTTGAGCATGATCCCAAATGC
AACTGCATTTTCAGATATTTCTGTACTCTTTTTCAAGTCACAAAACTAACAGCTCCATGTACAATCGTAGCTTTGGTGTA
TACTGAATGCCTTTTAACTAATGCTAACATTGATCTTTGTCCTACTAATTAGAAAAAAATTGTCCTTGGAGCCATGCTTC
TGGCCTCCAAGGTTTGGAGAAATCGTGGTCTGAGGAGTGTGGATGACAGCCAGAATCCCAAGGACGTTGCAGTTGAGAAA
ATGATTAAGATGGAGAAGCGTTTTTTTGGAGCTACTTGAGTTTAATATTCATGTGTCTGCCAGTGTTTATGCAAAACATT
ACTTTGACCTGCATGCCTTGGCAAATGACCATGACCTGTATTTTCTAATTAGTCTTCTTCATAAAGATAAAGCACAGAAA
TTGAAGGCTACGTCATGGCCATGTGAATACAAAGAGTTGCATCAAGATGTTGCTGCTATGACAAGGGCCATCAGCATGGA
TTTCATTGGTATTCCATGCACTAATGCCATCTTATCT

Alignment

ORF - retro_cjac_1164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.08 %
• Parental protein coverage: 98.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HHIRPRHLGRTYSSCSTILLDNSTVSEPELCHTLESVTLAIYYNIKHRTVYANRSLAIFNESIHPLSQEE
          ..I.P.HL...YSSCSTILLDNSTVS.P.L.H.LE.VTLAIYYNIKHR..YANRSL.IF.E.IH.LSQE.
Retrocopy YSICPWHLYIKYSSCSTILLDNSTVSKPDLSHMLENVTLAIYYNIKHR--YANRSLVIFDEPIHLLSQEK

Parental  IPGKSFEDDPTHKCIFSYFCNIFAVAELTAPCAIVALVYIERLLTKANIDLCPTNWKKIVLGAMLLASKV
          .PGKSFE.DP...CIF.YFC..F.V..LTAPC.IVALVY.E.LLT.ANIDLCPTN.KKIVLGAMLLASKV
Retrocopy TPGKSFEHDPKCNCIFRYFCTLFQVTKLTAPCTIVALVYTECLLTNANIDLCPTN*KKIVLGAMLLASKV

Parental  WRDRGLWSVDDSQNPKDVAVETMSKMEKS-FLELLEFKIHVSASVYVKYYFDLCALPYDHELDFQFSILH
          WR.RGL.SVDDSQNPKDVAVE.M.KMEK..FLELLEF.IHVSASVY.K.YFDL.AL..DH.L.F..S.LH
Retrocopy WRNRGLRSVDDSQNPKDVAVEKMIKMEKR>FLELLEFNIHVSASVYAKHYFDLHALANDHDLYFLISLLH

Parental  KHIAQKLKAMSRLCEYKDLHQDAAAMTRAISMDFIGIRHTNAILS
          K..AQKLKA.S..CEYK.LHQD.AAMTRAISMDFIGI..TNAILS
Retrocopy KDKAQKLKATSWPCEYKELHQDVAAMTRAISMDFIGIPCTNAILS

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	0.04 RPM	0.02 RPM
SRP051959_heart	1.18 RPM	0.04 RPM
SRP051959_kidney	0.22 RPM	0.02 RPM
SRP051959_liver	0.02 RPM	0.00 RPM
SRP051959_lung	0.03 RPM	0.15 RPM
SRP051959_lymph_node	0.05 RPM	0.27 RPM
SRP051959_skeletal_muscle	0.07 RPM	0.04 RPM
SRP051959_spleen	0.00 RPM	0.06 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1164 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1164 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001008	1 retrocopy	retro_cjac_3555,
Callithrix jacchus	ENSCJAG00000002901	1 retrocopy	retro_cjac_569,
Callithrix jacchus	ENSCJAG00000011445	1 retrocopy	retro_cjac_1164 ,
Callithrix jacchus	ENSCJAG00000034702	1 retrocopy	retro_cjac_610,
Homo sapiens	ENSG00000163249	3 retrocopies	retro_hsap_1629, retro_hsap_1984, retro_hsap_4845,
Gorilla gorilla	ENSGGOG00000008136	1 retrocopy	retro_ggor_1229,
Mus musculus	ENSMUSG00000070871	1 retrocopy	retro_mmus_3072,
Pan troglodytes	ENSPTRG00000008072	1 retrocopy	retro_ptro_1091,