RetrogeneDB ID: retro_cjac_1354

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:74346565..74347352(+)
• Located in intron of: ENSCJAG00000007930

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM56
• Ensembl ID: ENSCJAG00000018153
• Aliases: None
• Description: transmembrane protein 56 [Source:HGNC Symbol;Acc:26477]

Sequence

>retro_cjac_1354
ATGGATGTCAACACAAATTGTTCATCAGCATTAATTGTACCAGCTTTTTCACCTTTCAGCTTCTCTTCTACTTTGTAAGT
TACTGGTTTTCAGCAAAAGTTTCTCCAGGTTTCAATAGTCTTACCTTTGAAAAGAAGATTGAATGGAACTCAAGGGTAGT
ATCCACATGCCATTCTTTGGTGGTTGGTATTTTTGGCCTGTACATTTTCTTATTCGATGAGGCTACTAAAGCTGATCCAC
TCTAGGGTGATCCATTACTTGCAAACGTGAATATTGCTGTTGCTTCAGGCTACCTCATTTCTGATTTGTCCATTATACTT
TTGTATTGGAAAGTGATTGGTGACAAATTTTTTATAATACATCATTGTGCGGCCCTGTATGGATACTACTTTATACTGAA
AGATGGAGTGCTGGCATACGTCAGGAATTTCGCCTGCTTGCAGAGCTTTCCAGCCCTTTTGTGAATCAGCAGTGGTTCTT
TGAAGCTCTGAAGTATCCCAAGTTTTCCAAAGCTAATGTTATCGATGGAATACTCATGACAGTAGTGTTCTTCACCGTGA
GGACTGCCTCAAAGCCTCCTCTTTATGGCCTCATGTATTCTGTGTATGGAACAGAACCCTACATAAGGCTTGGATTTTTA
ATCCAGTGTTCCTGGATCATTAGTTGTGCTGTTTTGGATGTGATGAATGTCATGTGGATGATCAAAATTTCAAAAGGTTG
CATCAAAGTCATCTCTCTCATCAGACAAGAGAAGGCCAAAAATAGTCTTCAGAATGGAAAACTTGAT

Alignment

ORF - retro_cjac_1354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.96 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDVNT-KLFISIICTSFFTFQLLFYFVSYWFSAKVSPGFNSLTFEKKIEWNSRVVSTCHSLVVGIFGLYI
          MDVNT.KLFISI.CTSFFTFQLLFYFVSYWFSAKVSPGFNSLTFEKKIEWNSRVVSTCHSLVVGIFGLYI
Retrocopy MDVNT<KLFISINCTSFFTFQLLFYFVSYWFSAKVSPGFNSLTFEKKIEWNSRVVSTCHSLVVGIFGLYI

Parental  FLFDEATKADPLWGDPSLANVNIAIASGYLISDLFIIILYWKVIGDKFFVIHHCAALYGYYFILKDGVLA
          FLFDEATKADPL.GDP.LANVNIA.ASGYLISDL.II.LYWKVIGDKFF.IHHCAALYGYYFILKDGVLA
Retrocopy FLFDEATKADPL*GDPLLANVNIAVASGYLISDLSIILLYWKVIGDKFFIIHHCAALYGYYFILKDGVLA

Parental  YVGN-FRLLAELSSPFVNQRWFFEALKYPKFSKANVINGILMTVVFFTVRIASMPPLYGFMYSVYGTEPY
          YV.N.FRLLAELSSPFVNQ.WFFEALKYPKFSKANVI.GILMTVVFFTVR.AS.PPLYG.MYSVYGTEPY
Retrocopy YVRN<FRLLAELSSPFVNQQWFFEALKYPKFSKANVIDGILMTVVFFTVRTASKPPLYGLMYSVYGTEPY

Parental  IRLGFLIQCSWIISCAVLDVMNVMWMIKISKGCIKVISLIRQEKAKNNLQNGKLD
          IRLGFLIQCSWIISCAVLDVMNVMWMIKISKGCIKVISLIRQEKAKN.LQNGKLD
Retrocopy IRLGFLIQCSWIISCAVLDVMNVMWMIKISKGCIKVISLIRQEKAKNSLQNGKLD

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	3.19 RPM	4.30 RPM
SRP051959_heart	1.28 RPM	8.17 RPM
SRP051959_kidney	1.33 RPM	3.04 RPM
SRP051959_liver	1.23 RPM	17.59 RPM
SRP051959_lung	3.61 RPM	2.26 RPM
SRP051959_lymph_node	3.42 RPM	0.07 RPM
SRP051959_skeletal_muscle	0.55 RPM	4.08 RPM
SRP051959_spleen	6.72 RPM	2.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1354 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1354 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1354 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018153	1 retrocopy	retro_cjac_1354 ,
Otolemur garnettii	ENSOGAG00000002403	1 retrocopy	retro_ogar_687,