RetrogeneDB ID: retro_cjac_1433

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:91774146..91774866(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DKKL1
• Ensembl ID: ENSCJAG00000000102
• Aliases: None
• Description: dickkopf-like 1 [Source:HGNC Symbol;Acc:16528]

Sequence

>retro_cjac_1433
TCCCCGCCTGCCCCCGCAATGCGGCACCCACTAGTCCTGCCGCTGCTCCTCTCTGCCCTGGTGACCCCCTCCGCTGCAGC
ACCTATCCACGATGCTGATGCCCAAGAGAGCTCCTTTGGTCTTACAGGCCTCCGAAGCCTGCTCCAAGTCTTTAGCTGAC
TTTTCCTGAAACAGCAGGATGATCTGCTTTGGGGCATGGACAGCTTCTTCTCTGCCCTCATGGACTTCTGGGGCCTCCCT
AGGAACTACCACCAAGAGGGGAACCAGGAGCACCAGCTGGGAAACAACACCATCTCCAGCCACCTCCAGATCGACAAGGT
GACAGACAACAAGACAGGAGAGGTGCTGATCTCTGAGAAGGTGGTGGCATCCATCCAACTAGCAGAGGGGAGCTTCAAGG
GTGACAGGAAGGTACCCAGGATGGAGGAGAAGGAGGCCCTGGTGCCAATCTGAAAGGCCATGAACAGCTTCCACACAGAA
CTCTGTCCCCAGGTGGCCTTCTGGATCATGAAGCTGCCATGGCAGAGGTCCCACCAGGATGTCCCAGAGGGTGGCCACTG
GCTCAGCGAGAAGTGACACCGCCTGCAGGCCATCCGAGATGGGCTCCATGAGGGGACCCGTGAGGACGTCTTAGAAGAGA
GGACCCAGGGCTTCTCCCACTCCAGGCTGTTCCCCCAAAAGACCCACTTACCCTACATCTTTAGGCCCTCCCAGCAGCTG

Alignment

ORF - retro_cjac_1433 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPPVPAMRHPLVLLLLLSALVSPSTAAPIHHADAQESSFGLTGLQSLLQVFSRLFLKPQDDLLRGMDSFF
          SPP.PAMRHPLVL.LLLSALV.PS.AAPIH.ADAQESSFGLTGL.SLLQVFS.LFLK.QDDLL.GMDSFF
Retrocopy SPPAPAMRHPLVLPLLLSALVTPSAAAPIHDADAQESSFGLTGLRSLLQVFS*LFLKQQDDLLWGMDSFF

Parental  SAPMDFRGLPRNYHQEENQEHQLGNNTISSHLQIDKVTDNKTGDVLISEKVVASIQPAEGSFKGDWKVPR
          SA.MDF.GLPRNYHQE.NQEHQLGNNTISSHLQIDKVTDNKTG.VLISEKVVASIQ.AEGSFKGD.KVPR
Retrocopy SALMDFWGLPRNYHQEGNQEHQLGNNTISSHLQIDKVTDNKTGEVLISEKVVASIQLAEGSFKGDRKVPR

Parental  MEEKEALVPIQKAMNSYHAELHPRVAFWIMKLPRQRSHQDVPEGGHWLSEKRHRLQAIRDGLREGTRDDV
          MEEKEALVPI.KAMNS.H.EL.P.VAFWIMKLP.QRSHQDVPEGGHWLSEK.HRLQAIRDGL.EGTR.DV
Retrocopy MEEKEALVPI*KAMNSFHTELCPQVAFWIMKLPWQRSHQDVPEGGHWLSEK*HRLQAIRDGLHEGTREDV

Parental  LEERTQGFSHFRLFPRKTHLLYIFRPSRQL
          LEERTQGFSH.RLFP.KTHL.YIFRPS.QL
Retrocopy LEERTQGFSHSRLFPQKTHLPYIFRPSQQL

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	0.02 RPM	0.09 RPM
SRP051959_heart	0.04 RPM	0.05 RPM
SRP051959_kidney	0.13 RPM	0.18 RPM
SRP051959_liver	0.06 RPM	0.15 RPM
SRP051959_lung	0.10 RPM	0.13 RPM
SRP051959_lymph_node	0.09 RPM	0.07 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.02 RPM
SRP051959_spleen	0.02 RPM	0.02 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1433 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1433 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1433 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	ENSCJAG00000000102	1 retrocopy	retro_cjac_1433 ,
Homo sapiens	ENSG00000104901	1 retrocopy	retro_hsap_2421,
Gorilla gorilla	ENSGGOG00000016382	1 retrocopy	retro_ggor_1506,
Macaca mulatta	ENSMMUG00000014794	1 retrocopy	retro_mmul_627,
Pan troglodytes	ENSPTRG00000011292	1 retrocopy	retro_ptro_1395,