RetrogeneDB ID: retro_cjac_1900

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:36464124..36464898(-)
• Located in intron of: ENSCJAG00000016883

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRM
• Ensembl ID: ENSCJAG00000019904
• Aliases: None
• Description: nurim (nuclear envelope membrane protein) [Source:HGNC Symbol;Acc:8003]

Sequence

>retro_cjac_1900
ATGGCCCCTGCACTGCTCCTGGTCCCTGCTGCCCTCGCCTCTTTCATCCTAGCCTTTGGCACTGGAGTGGAGTTTACGCA
CTTTACCTCCCTTCAGTCACTTCTTGGAGGGATCCCAGAGTCTGGTGGTCCCAATGCCTGACAGGGATGGCTGGCTGCCC
TGCAGGACCGCAGCATCCTTGCCCCCCTGGCATGGGATCTGGGGCTCCTGCTTCTATTTGTTGGGCAGCACAGCCTCATA
GCAGCTGAGAGAGTGAAACCATGGCCATCCCGGTACTTTGGGGTCCTTCAGAGGTCACTGTATGTGGCCTGCACTGCCCT
GGCCTTGCAGCTGGTGATGCGGTACTGGGAGCCTGTACCCAGAGGCCCCGTGTTGTGGGAGGCTCGAGCTGAGCCATGGG
CCACCTGGGTGCCCCTCCTCTGCTTTGTGCTCCATATCATCTCCTGGCTCCTCATCTTCAGCATCCTTCTCGTCTTTGAC
TACACTGAGCTCATGGGCCTCAAACAGGTGTACTACCATGTGCTGGGGCTGGGCGAGCCTCTGGCCCTGAAGTCTCCCCG
GGCTCTCAGTCTCTTCTCCCACCTGCGCCACCCAGTGTGTGTGGAGCTGCTGACAGTGCTGTGGGTGGTGCCTACGCTTG
GCACAGACCATCTCCTCCTTACCCTCTACCTGGGCCTGGCTCATAGGCTTGATCAGCAAGACCTCTGCTACCTCCGGGCC
CAGCTGCAAAGAAAACTCCACCTGCTCTCTCGACCCCAGGATGGGGAGGCAGAG

Alignment

ORF - retro_cjac_1900 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPALLLVPAALASFILAFGTGVEFVRFASLQPLLGGIPESVGPDARQGWLAALQDRSILAPLAWDLGLL
          MAPALLLVPAALASFILAFGTGVEF..F.SLQ.LLGGIPES.GP.A.QGWLAALQDRSILAPLAWDLGLL
Retrocopy MAPALLLVPAALASFILAFGTGVEFTHFTSLQSLLGGIPESGGPNA*QGWLAALQDRSILAPLAWDLGLL

Parental  LLFVGQHSLMAAERVKAWTSRYFGVLQRSLYVACTALALQLVMRYWEPIPRGPVLWEARAEPWATWVPLL
          LLFVGQHSL.AAERVK.W.SRYFGVLQRSLYVACTALALQLVMRYWEP.PRGPVLWEARAEPWATWVPLL
Retrocopy LLFVGQHSLIAAERVKPWPSRYFGVLQRSLYVACTALALQLVMRYWEPVPRGPVLWEARAEPWATWVPLL

Parental  CFVLHVISWLLIFSILLVFDYAELMGLKQVYYHVLGLGEPLALKSPRALRLFSHLRHPVCVELLTVLWVV
          CFVLH.ISWLLIFSILLVFDY.ELMGLKQVYYHVLGLGEPLALKSPRAL.LFSHLRHPVCVELLTVLWVV
Retrocopy CFVLHIISWLLIFSILLVFDYTELMGLKQVYYHVLGLGEPLALKSPRALSLFSHLRHPVCVELLTVLWVV

Parental  PTLGTDRLLLALLLTLYLGLAHGLDQQDLRYLRAQLQRKLHLLSRPQDGEAE
          PTLGTD.LLL....TLYLGLAH.LDQQDL.YLRAQLQRKLHLLSRPQDGEAE
Retrocopy PTLGTDHLLL----TLYLGLAHRLDQQDLCYLRAQLQRKLHLLSRPQDGEAE

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	2.13 RPM	1.24 RPM
SRP051959_heart	1.61 RPM	2.17 RPM
SRP051959_kidney	2.17 RPM	1.20 RPM
SRP051959_liver	1.04 RPM	0.80 RPM
SRP051959_lung	2.20 RPM	3.48 RPM
SRP051959_lymph_node	4.00 RPM	2.40 RPM
SRP051959_skeletal_muscle	1.55 RPM	1.35 RPM
SRP051959_spleen	1.87 RPM	1.97 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1900 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1900 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1900 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019904	1 retrocopy	retro_cjac_1900 ,