RetrogeneDB ID: retro_cjac_1412

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:74554044..74554313(-)
• Located in intron of: ENSCJAG00000008033

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000005727
• Aliases: None
• Description: None

Sequence

>retro_cjac_1412
AGGAAGGTAAGCTCAGCAGAAGGAGTAGTGAAGGAAGAGCCCAAGAGGAGACCTGATGTGGTTCTCAGTTAACCCTGCTC
CTACAAAAGTGGAAAGGAAGACAAAAAAAAAGGCAGCAGGAAAAGATAAATCTTCAGACAAAAGAAAAATGAGAAGGAGA
GCAAAGAGAAAATGGAGAGAAGTGGCTAACCAAGAAACTAAAGATTTACCTACAGAAAACAAGAGAAACCAAAACTGAGG
AGGCTCCAGTCTCTGAGAAAGCCAGAGAA

Alignment

ORF - retro_cjac_1412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.06 %
• Parental protein coverage: 90.91 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RKVSSAEGAAKEEPKRRSARLSAKPPAKVEAK--PKKAAAK-DKSSDKKVQTKGKRGAKGKQAEVAKETK
          RKVSSAEG..KEEPKRR.......P......K...KK...K.DKSSDK....K..R.AK.K..EVA....
Retrocopy RKVSSAEGVVKEEPKRRPDVVLS*PCSYKSGKEDKKKGSRK>DKSSDKR---KMRRRAKRKWREVANQET

Parental  EDLPAEN-GETKIEESPASDEAGE
          .DLP.EN..ETK.EE.P.S..A.E
Retrocopy KDLPTEN>RETKTEEAPVSEKARE

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	0.13 RPM	38.63 RPM
SRP051959_heart	0.14 RPM	18.86 RPM
SRP051959_kidney	0.13 RPM	49.03 RPM
SRP051959_liver	0.13 RPM	33.12 RPM
SRP051959_lung	0.23 RPM	40.93 RPM
SRP051959_lymph_node	0.11 RPM	73.12 RPM
SRP051959_skeletal_muscle	0.15 RPM	6.46 RPM
SRP051959_spleen	0.17 RPM	39.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1412 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1412 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1821
Pongo abelii	retro_pabe_2284

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005727	4 retrocopies	retro_cjac_1105, retro_cjac_1412 , retro_cjac_2018, retro_cjac_4230,
Gorilla gorilla	ENSGGOG00000013672	6 retrocopies	retro_ggor_107, retro_ggor_145, retro_ggor_16, retro_ggor_2248, retro_ggor_48, retro_ggor_49,
Otolemur garnettii	ENSOGAG00000033084	3 retrocopies	retro_ogar_1799, retro_ogar_2793, retro_ogar_3104,
Tarsius syrichta	ENSTSYG00000005812	15 retrocopies	retro_tsyr_1029, retro_tsyr_1109, retro_tsyr_1203, retro_tsyr_1209, retro_tsyr_1243, retro_tsyr_1318, retro_tsyr_1904, retro_tsyr_1956, retro_tsyr_310, retro_tsyr_399, retro_tsyr_652, retro_tsyr_664, retro_tsyr_680, retro_tsyr_728, retro_tsyr_913,
Tursiops truncatus	ENSTTRG00000015372	12 retrocopies	retro_ttru_1034, retro_ttru_129, retro_ttru_1511, retro_ttru_1682, retro_ttru_1714, retro_ttru_200, retro_ttru_337, retro_ttru_373, retro_ttru_558, retro_ttru_61, retro_ttru_680, retro_ttru_980,
Vicugna pacos	ENSVPAG00000000013	7 retrocopies	retro_vpac_146, retro_vpac_216, retro_vpac_248, retro_vpac_371, retro_vpac_499, retro_vpac_557, retro_vpac_66,