RetrogeneDB ID: retro_cjac_985

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 12:67661905..67662523(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP2CB
• Ensembl ID: ENSCJAG00000012460
• Aliases: None
• Description: Serine/threonine-protein phosphatase [Source:UniProtKB/TrEMBL;Acc:F6XZ20]

Sequence

>retro_cjac_985
AAAGTGCGTTATCCACAATGCATTACGATATTGAGAGGAAATCACGAAAGCCGACAAATTACTCAAGTATATGGCTTTTA
TGATGAATGTCTGTGAAAGTATGGAAATGCTAATGTTTGGAAATATTTTACAGATCTCTTTGATTATCTTCCACTTACAG
CTTTAGTAGATAGGCAGATATTCTGCCTCCATGGTGGCCTCCCTCCATCCACAGACAAACTGGATCATATAAGAACCCTG
GATCGTTCACAGGAAGTTCCACATGAGGGCCCAATGTGTGATCTGTTATGGTCAGATCCAGATGATCGTGGTGGATGGGG
TATTTCACCACGTAGTGCTGGCTACACGCTCGGACAAGACATTTCTGAAACCTTTAACCATGCCAATGGTCTCACACTGG
TTTCTCGTGCCCACCAGCTTGTAATGGAGGGATACAATTGGTGTCATGTTCGGAATGTGGTTACCATTTTCAGTGCACCC
AATTACTGTTATCGTTTTGGGAACCAGGCTGCTATCATGGAATTAGATGACACTTTAAAATATTCCTTCCTTCAGTTTGA
CCCAGCACTCCGTCGTGGCGAGCCTCATGTTACGCGGCGCACCCCAGACTACTTCCTA

Alignment

ORF - retro_cjac_985 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.2 %
• Parental protein coverage: 66.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVRYPERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPS
          KVRYP..ITILRGNHESRQITQVYGFYDECL.KYGNANVWKYFTDLFDYLPLTALVD.QIFCLHGGL.PS
Retrocopy KVRYPQCITILRGNHESRQITQVYGFYDECL*KYGNANVWKYFTDLFDYLPLTALVDRQIFCLHGGLPPS

Parental  IDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQL
          .D.LDHIR.LDR.QEVPHEGPMCDLLWSDPDDRGGWGISPR.AGYT.GQDISETFNHANGLTLVSRAHQL
Retrocopy TDKLDHIRTLDRSQEVPHEGPMCDLLWSDPDDRGGWGISPRSAGYTLGQDISETFNHANGLTLVSRAHQL

Parental  VMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRRTPDYFL
          VMEGYNWCH.RNVVTIFSAPNYCYR.GNQAAIMELDDTLKYSFLQFDPA.RRGEPHVTRRTPDYFL
Retrocopy VMEGYNWCHVRNVVTIFSAPNYCYRFGNQAAIMELDDTLKYSFLQFDPALRRGEPHVTRRTPDYFL

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	29.60 RPM
SRP051959_heart	0.00 RPM	22.52 RPM
SRP051959_kidney	0.00 RPM	33.12 RPM
SRP051959_liver	0.02 RPM	9.55 RPM
SRP051959_lung	0.02 RPM	24.82 RPM
SRP051959_lymph_node	0.05 RPM	10.30 RPM
SRP051959_skeletal_muscle	0.04 RPM	11.31 RPM
SRP051959_spleen	0.06 RPM	17.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_985 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_985 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_985 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012460	1 retrocopy	retro_cjac_985 ,
Callithrix jacchus	ENSCJAG00000013634	2 retrocopies	retro_cjac_1346, retro_cjac_4113,
Dasypus novemcinctus	ENSDNOG00000010906	1 retrocopy	retro_dnov_2211,
Homo sapiens	ENSG00000104695	1 retrocopy	retro_hsap_1631,
Gorilla gorilla	ENSGGOG00000013978	1 retrocopy	retro_ggor_380,
Macaca mulatta	ENSMMUG00000020819	1 retrocopy	retro_mmul_484,
Monodelphis domestica	ENSMODG00000019001	2 retrocopies	retro_mdom_192, retro_mdom_632,
Oryctolagus cuniculus	ENSOCUG00000005230	1 retrocopy	retro_ocun_1697,
Pongo abelii	ENSPPYG00000018491	1 retrocopy	retro_pabe_335,