RetrogeneDB ID: retro_cjac_3061

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 8:34853641..34854086(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000001265
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000010356
• Aliases: None
• Description: None

Sequence

>retro_cjac_3061
ATGTTTCTCATGATCCCTGAAAAGTTCTAGCATATTTTATTACTTGACACCAACATCGATGGGGGTTGGAAAATAGCCTT
TGCCATCACTGCCATTAAGGGTATGGGTCAAAGATATGCTCATGTGGTATTGGGGAAAGCAGACGTCGACCTTACCAAGA
GTGCAGGAGAACTGACAGGGAATGAGTTGGAATGTATGATCACCATTATGCAGAATCTATGCCAATTCAAGATCCCAAAC
TCGTTCTTGAACAGACAGAGAGACGTAATGGATGGAAAATATAGGCAGGTCCTAGCCAATGGTCTGGACAACAAGTTCTG
TGAAGACCTGGAGCGACTGAAGATTTGGGCCCATCTCCATGGACTTTTGGAGCCTTTGCGTTTGAGGCCAGCACACCAAG
ACCACTGGCCACCATGATCATACTGTGGGTGTGTCTAAGAAAAAA

Alignment

ORF - retro_cjac_3061 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSLVIPEKFQDILRVLNTNIDGRRKIAFAITTIKGVDRRHAHVVLRKADIAFTKRAGELTEDEVERVITI
          M.L.IPEKF..IL..L.TNIDG..KIAFAIT.IKG...R.AHVVL.KAD...TK.AGELT..E.E..ITI
Retrocopy MFLMIPEKF*HIL-LLDTNIDGGWKIAFAITAIKGMGQRYAHVVLGKADVDLTKSAGELTGNELECMITI

Parental  MQNPRQYKIPDWFLNRQKDVKDGKYNQFLANGLDNKLRENLERLKKIRAHRGLH-HFWGLRVRGQHTKTT
          MQN..Q.KIP..FLNRQ.DV.DGKY.Q.LANGLDNK..E.LERL.KI.AH..LH..FW.L.V.GQHTKTT
Retrocopy MQNLCQFKIPNSFLNRQRDVMDGKYRQVLANGLDNKFCEDLERL-KIWAH--LH>DFWSLCV*GQHTKTT

Parental  GHRGRTVGVSKKK
          GH...TVGVSKKK
Retrocopy GHHDHTVGVSKKK

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	0.53 RPM
SRP051959_heart	0.00 RPM	0.40 RPM
SRP051959_kidney	0.00 RPM	0.53 RPM
SRP051959_liver	0.00 RPM	0.71 RPM
SRP051959_lung	0.00 RPM	0.60 RPM
SRP051959_lymph_node	0.00 RPM	0.94 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.50 RPM
SRP051959_spleen	0.00 RPM	0.55 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3061 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3061 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3061 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3070

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010356	1 retrocopy	retro_cjac_3061 ,
Callithrix jacchus	ENSCJAG00000021650	5 retrocopies	retro_cjac_22, retro_cjac_245, retro_cjac_2529, retro_cjac_2893, retro_cjac_2955,
Loxodonta africana	ENSLAFG00000032173	1 retrocopy	retro_lafr_1171,
Monodelphis domestica	ENSMODG00000014210	4 retrocopies	retro_mdom_1041, retro_mdom_1286, retro_mdom_1514, retro_mdom_642,
Tarsius syrichta	ENSTSYG00000012508	8 retrocopies	retro_tsyr_1121, retro_tsyr_1307, retro_tsyr_1627, retro_tsyr_194, retro_tsyr_1949, retro_tsyr_2042, retro_tsyr_575, retro_tsyr_639,