RetrogeneDB ID: retro_cjac_3178

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:8703298..8703558(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000012417
• Aliases: None
• Description: None

Sequence

>retro_cjac_3178
GCTAAATGCACCAATATAGTTGGAATTCTCAGTAAATACAGGACCCGCTATGGTGCCTCCCTCCAGAAAATGGTGAAAAA
TACTGAAACCAGCCAGCACACCGAGTACACTTGCTCTCTCTGTGGCAAAACCAAGAAGAAAAGATGAGATTCAGGGATCT
GGCACTGTGGTTCCTGCATGAAAACAGTAGCTGGTGGTGGCTGAACCTAAAATACCACTTCTGCTGGCATTTAAAGTCTG
CCATCAGAAGACTGAAGCAA

Alignment

ORF - retro_cjac_3178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.59 %
• Parental protein coverage: 94.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AKRTKKVGIVGKYGTRYGASLRKMVKKIEISQHAKYTCSFCGKTKMKRRAVGIWHCGSCMKTVAGGAWTY
          AK.T..VGI..KY.TRYGASL.KMVK..E.SQH..YTCS.CGKTK.KR...GIWHCGSCMKTVAGG..T.
Retrocopy AKCTNIVGILSKYRTRYGASLQKMVKNTETSQHTEYTCSLCGKTKKKR*DSGIWHCGSCMKTVAGGG*T*

Parental  NTTSAVT-VKSAIRRLKE
          NTTSA....KSAIRRLK.
Retrocopy NTTSAGI<LKSAIRRLKQ

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	55.78 RPM
SRP051959_heart	0.02 RPM	72.97 RPM
SRP051959_kidney	0.00 RPM	66.85 RPM
SRP051959_liver	0.02 RPM	77.00 RPM
SRP051959_lung	0.02 RPM	66.71 RPM
SRP051959_lymph_node	0.00 RPM	110.57 RPM
SRP051959_skeletal_muscle	0.02 RPM	118.82 RPM
SRP051959_spleen	0.00 RPM	91.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3178 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3178 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3178 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003377	24 retrocopies	retro_amel_109, retro_amel_1170, retro_amel_1197, retro_amel_1204, retro_amel_1248, retro_amel_1310, retro_amel_1349, retro_amel_1534, retro_amel_1597, retro_amel_1724, retro_amel_1815, retro_amel_1910, retro_amel_1929, retro_amel_248, retro_amel_424, retro_amel_428, retro_amel_475, retro_amel_482, retro_amel_606, retro_amel_737, retro_amel_809, retro_amel_83, retro_amel_920, retro_amel_942,
Callithrix jacchus	ENSCJAG00000012417	7 retrocopies	retro_cjac_1060, retro_cjac_1514, retro_cjac_159, retro_cjac_237, retro_cjac_3178 , retro_cjac_335, retro_cjac_888,
Equus caballus	ENSECAG00000012046	6 retrocopies	retro_ecab_220, retro_ecab_48, retro_ecab_552, retro_ecab_735, retro_ecab_741, retro_ecab_803,
Latimeria chalumnae	ENSLACG00000011578	1 retrocopy	retro_lcha_71,
Loxodonta africana	ENSLAFG00000006849	5 retrocopies	retro_lafr_1010, retro_lafr_1015, retro_lafr_109, retro_lafr_987, retro_lafr_991,
Macropus eugenii	ENSMEUG00000004680	23 retrocopies	retro_meug_1094, retro_meug_111, retro_meug_1120, retro_meug_1289, retro_meug_1302, retro_meug_1399, retro_meug_1600, retro_meug_1705, retro_meug_2021, retro_meug_2061, retro_meug_2143, retro_meug_2173, retro_meug_24, retro_meug_290, retro_meug_458, retro_meug_463, retro_meug_496, retro_meug_502, retro_meug_571, retro_meug_691, retro_meug_813, retro_meug_814, retro_meug_83,
Myotis lucifugus	ENSMLUG00000000762	1 retrocopy	retro_mluc_208,
Petromyzon marinus	ENSPMAG00000000001	1 retrocopy	retro_pmar_11,