RetrogeneDB ID: retro_cjac_1492

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:96741741..96742073(+)
• Located in intron of: ENSCJAG00000005084

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX7A2L
• Ensembl ID: ENSCJAG00000014705
• Aliases: None
• Description: cytochrome c oxidase subunit VIIa polypeptide 2 like [Source:HGNC Symbol;Acc:2289]

Sequence

>retro_cjac_1492
ATGTACTACAAATTTAGTGGCTTCATGCAGAAGTTGGTGGGAGCATGGGCTTCGGAGGCCTATAGCCCTCAGGGAAAGCC
TGTGGTTTTCACAGAAGCACCACTTACCATATTTGCCACACCAACTAAACTGACCTCCAATTCCACAGCATAGGATTATG
CTGGGAAAAACAAAGTTCCAGAGCTGCAGAATTTTTTCCAGAATGCTGATGGTACGCTCATCCACCCAAAATGAGGCCTG
CCTGACCAAATACTTAACCAACCACCATGGTGCTGACCATCGGAGAGATCATCTCCTGCCTGATTGCCCTCTAAGTGGCT
TCGCAGCCCAAA

Alignment

ORF - retro_cjac_1492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.34 %
• Parental protein coverage: 99.12 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MYYKFSGFTQKLAGAWASEAYSPQGLKPVVPTEAPPIIFATPTKLTSDSTVYDYAGKNRVPELQKFFQKA
          MYYKFSGF.QKL.GAWASEAYSPQG.KPVV.TEAP..IFATPTKLTS.ST..DYAGKN.VPELQ.FFQ.A
Retrocopy MYYKFSGFMQKLVGAWASEAYSPQG-KPVVFTEAPLTIFATPTKLTSNSTA*DYAGKNKVPELQNFFQNA

Parental  DGVPIYLKRGLPDQMLYR-TTMALTVGGTIYCLIALYMAAQPK
          DG..I..K.GLPDQ.L...TTM.LT.G..I.CLIAL..A.QPK
Retrocopy DGTLIHPK*GLPDQILNQ<TTMVLTIGEIISCLIAL*VASQPK

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	0.00 RPM	19.06 RPM
SRP051959_heart	0.00 RPM	22.63 RPM
SRP051959_kidney	0.00 RPM	29.09 RPM
SRP051959_liver	0.00 RPM	25.39 RPM
SRP051959_lung	0.00 RPM	17.29 RPM
SRP051959_lymph_node	0.00 RPM	17.76 RPM
SRP051959_skeletal_muscle	0.00 RPM	32.45 RPM
SRP051959_spleen	0.00 RPM	17.52 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1492 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1492 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1492 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010305	2 retrocopies	retro_cjac_1523, retro_cjac_4129,
Callithrix jacchus	ENSCJAG00000014705	1 retrocopy	retro_cjac_1492 ,
Echinops telfairi	ENSETEG00000011940	1 retrocopy	retro_etel_650,
Macaca mulatta	ENSMMUG00000016278	1 retrocopy	retro_mmul_110,
Mustela putorius furo	ENSMPUG00000008875	1 retrocopy	retro_mputfur_97,
Mus musculus	ENSMUSG00000024248	2 retrocopies	retro_mmus_32, retro_mmus_926,
Oryctolagus cuniculus	ENSOCUG00000027189	3 retrocopies	retro_ocun_1617, retro_ocun_1781, retro_ocun_28,
Otolemur garnettii	ENSOGAG00000016029	1 retrocopy	retro_ogar_114,
Ictidomys tridecemlineatus	ENSSTOG00000012922	1 retrocopy	retro_itri_21,