RetrogeneDB ID: retro_cjac_1472

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 16:51539962..51540560(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000021456
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZMAT2
• Ensembl ID: ENSCJAG00000016231
• Aliases: None
• Description: zinc finger, matrin-type 2 [Source:HGNC Symbol;Acc:26433]

Sequence

>retro_cjac_1472
ATGGCGTCGGGCAGCGGGACAAAAAACTTGGACTTTCGCCGAAAGTGGGACAAAGATGAGTACGAGAAGCTCGCCGAGAA
GAGGCTCACGGAAGAGAGAGAAAAGAAGGATGGAAAACCAGTGCAGCCTGTCAAGCGAGAGCTTCTACGGCATAGGGACT
ACAAGGTGGACTTGGAATCCAAACTTGGGAAGACAATTGTTATTACCAAGACCACACCTCAATCTGAGATGGGAGGATAT
TATTGCAATGTCTGTGACTGTGTGGTGAAGGACTCCATCAACTTTCTGGATCACATTAATGGAAAGAAACATCAGAGAAA
CCTGGGCATGTGTATGCGTGTGGAACGTTCCACCCTGGATCAGGTGAAGAAACGTTTTGAGGTCAACAAGAAGAAGATGG
AAGAAAAGCAGAAGGATTATGATTTTGAGGAAAGGATGAAGGAGCTCGGAGAAGAGGAGGAAAAGGCCAAAGCATACAAG
AAAGAGAAACAGAAGGAGAAGAAAAGGGAGGGCTGAGGAGGACTTGACATTTGAGGAGGATGATGAGATGGCAGCTGTGA
TGGGCTTCTCTGACTTTGGTTCCACCAAGAAGAGTTAC

Alignment

ORF - retro_cjac_1472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASGSGTKNLDFRRKWDKDEYEKLAEKRLTEEREKKDGKPVQPVKRELLRHRDYKVDLESKLGKTIVITK
          MASGSGTKNLDFRRKWDKDEYEKLAEKRLTEEREKKDGKPVQPVKRELLRHRDYKVDLESKLGKTIVITK
Retrocopy MASGSGTKNLDFRRKWDKDEYEKLAEKRLTEEREKKDGKPVQPVKRELLRHRDYKVDLESKLGKTIVITK

Parental  TTPQSEMGGYYCNVCDCVVKDSINFLDHINGKKHQRNLGMSMRVERSTLDQVKKRFEVNKKKMEEKQKDY
          TTPQSEMGGYYCNVCDCVVKDSINFLDHINGKKHQRNLGM.MRVERSTLDQVKKRFEVNKKKMEEKQKDY
Retrocopy TTPQSEMGGYYCNVCDCVVKDSINFLDHINGKKHQRNLGMCMRVERSTLDQVKKRFEVNKKKMEEKQKDY

Parental  DFEERMKELREEEEKAKAYKKEKQKEKKR-RAEEDLTFEEDDEMAAVMGFSGFGSTKKSY
          DFEERMKEL.EEEEKAKAYKKEKQKEKKR.RAEEDLTFEEDDEMAAVMGFS.FGSTKKSY
Retrocopy DFEERMKELGEEEEKAKAYKKEKQKEKKR>RAEEDLTFEEDDEMAAVMGFSDFGSTKKSY

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	0.07 RPM	10.38 RPM
SRP051959_heart	0.09 RPM	16.63 RPM
SRP051959_kidney	0.07 RPM	19.77 RPM
SRP051959_liver	0.06 RPM	15.16 RPM
SRP051959_lung	0.02 RPM	20.37 RPM
SRP051959_lymph_node	0.00 RPM	18.20 RPM
SRP051959_skeletal_muscle	0.02 RPM	22.38 RPM
SRP051959_spleen	0.06 RPM	20.82 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1472 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1472 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1472 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005907	1 retrocopy	retro_cfam_822,
Callithrix jacchus	ENSCJAG00000016231	3 retrocopies	retro_cjac_1137, retro_cjac_1472 , retro_cjac_4007,
Dipodomys ordii	ENSDORG00000014559	8 retrocopies	retro_dord_123, retro_dord_127, retro_dord_129, retro_dord_131, retro_dord_133, retro_dord_135, retro_dord_136, retro_dord_138,
Echinops telfairi	ENSETEG00000005406	2 retrocopies	retro_etel_156, retro_etel_882,
Ficedula albicollis	ENSFALG00000008988	1 retrocopy	retro_falb_9,
Myotis lucifugus	ENSMLUG00000017525	2 retrocopies	retro_mluc_2281, retro_mluc_2309,
Monodelphis domestica	ENSMODG00000011269	1 retrocopy	retro_mdom_1209,
Pteropus vampyrus	ENSPVAG00000009717	1 retrocopy	retro_pvam_827,
Tursiops truncatus	ENSTTRG00000001777	4 retrocopies	retro_ttru_1889, retro_ttru_340, retro_ttru_721, retro_ttru_766,