RetrogeneDB ID: retro_cjac_4077

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:65793633..65794040(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000010581
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SHISA5
• Ensembl ID: ENSCJAG00000002915
• Aliases: None
• Description: shisa homolog 5 (Xenopus laevis) [Source:HGNC Symbol;Acc:30376]

Sequence

>retro_cjac_4077
ATGGGATTCGGAGCAACTGTGGCCATCGGTCTCACCATCTTTGTGCTGTCTGTCATCACTATCTTCATCTGCTTCACCTG
CTCCTGCTGCTGCCTGTACGAGATGTGCTGCCAACCACATCAGGTTGTTACCACCATCACATTCACCACTGTGGTGCACG
CCCCTTACACTCAGTTTCCAAGTGTGCTGCCCAGCTACCCTTGACTGAGCTACAAGAGCTACCACCACATTCCCCCCAGC
CAGGGATGCCAGCAGCACCCTATCCAATGCAGTACCCACCACTTTACCTGGTCCAGTCCATGGGACCGCCGGTCTACCAC
AAGACCCTGGCTGGAGGAGCAGCCGTGCCCTACCCTGCTAGTCAGCCTCTTCACAACCAAGCCTATATAAATGCCCCAAA
GGTGTCC

Alignment

ORF - retro_cjac_4077 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.99 %
• Parental protein coverage: 99.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGFGATLAVGLTIFVLSVVTIIICFTCSCCCLYKTCCQPRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPS
          MGFGAT.A.GLTIFVLSV.TI.ICFTCSCCCLY..CCQP..VVTT.T.TTVVHAPY.Q.PSV.PSYP..S
Retrocopy MGFGATVAIGLTIFVLSVITIFICFTCSCCCLYEMCCQPHQVVTTITFTTVVHAPYTQFPSVLPSYP*LS

Parental  YQGYHAMP-PQPGMPAAPYPMQYPPPYPAQPMGPPACHETLAGGVAAPYSASQPPYNPAYMDAPKAA
          Y..YH..P.PQPGMPAAPYPMQYPP.Y..Q.MGPP..H.TLAGG.A.PY.ASQP..N.AY..APK..
Retrocopy YKSYHHIP<PQPGMPAAPYPMQYPPLYLVQSMGPPVYHKTLAGGAAVPYPASQPLHNQAYINAPKVS

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	0.27 RPM	7.34 RPM
SRP051959_heart	1.18 RPM	5.44 RPM
SRP051959_kidney	0.89 RPM	14.73 RPM
SRP051959_liver	0.45 RPM	8.97 RPM
SRP051959_lung	1.32 RPM	24.81 RPM
SRP051959_lymph_node	0.48 RPM	30.07 RPM
SRP051959_skeletal_muscle	0.52 RPM	2.73 RPM
SRP051959_spleen	1.18 RPM	13.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_4077 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_4077 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_4077 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4706
Pan troglodytes	retro_ptro_3128
Pongo abelii	retro_pabe_3653

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002915	2 retrocopies	retro_cjac_4077 , retro_cjac_4152,
Homo sapiens	ENSG00000164054	2 retrocopies	retro_hsap_4706, retro_hsap_4812,
Gorilla gorilla	ENSGGOG00000028207	2 retrocopies	retro_ggor_2996, retro_ggor_86,
Macaca mulatta	ENSMMUG00000010062	1 retrocopy	retro_mmul_2565,
Nomascus leucogenys	ENSNLEG00000006485	1 retrocopy	retro_nleu_1984,
Pongo abelii	ENSPPYG00000013902	3 retrocopies	retro_pabe_2120, retro_pabe_3653, retro_pabe_3739,
Pan troglodytes	ENSPTRG00000014888	1 retrocopy	retro_ptro_3128,