RetrogeneDB ID: retro_cjac_2018

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 21:4271130..4271428(+)
• Located in intron of: ENSCJAG00000008622

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_2018
ATGCCCCAGAGGAAGGTCAGCTCAGCCGAAGGGGTGGTGAAGGAAGAACCCAAGAAGATCTGCACACTTGTCAGCTAAAC
CTGCTCCTGCAAAAGTGGAAACCAAGCCAAAATGGCATCAGGAAAGGATAAATATTCAGATTAAAAAAAATGCAAACAAA
ACGGAACAGGGGAGCAAAGGGCAAACAGGCCGAAGTGGCTAACCAGCAAACTGAAGATCTACCTGCAGAAACGAAGCAAC
TAAAACCGAGGAGAAGCCAACCTCTGATGAAGCAGGAGAGAAAGAAGCCAAGTCTGAT

Alignment

ORF - retro_cjac_2018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPKRKVSSAEGAAKEEPKRRSARLS-AKPPAKVEAKP-KKAAAKDKSSD-KK-VQTKGKRGAKGKQAEVA
          MP.RKVSSAEG..KEEPK......S....PAKVE.KP.K.A..KDK.SD.KK..QTK..RGAKGKQAEVA
Retrocopy MPQRKVSSAEGVVKEEPKKICTLVS>KPAPAKVETKP<KMASGKDKYSD*KK<MQTKRNRGAKGKQAEVA

Parental  KETKEDLPAE-NGETKIEESPASDEAGEKEAKSD
          ....EDLPAE.N..TK.EE.P.SDEAGEKEAKSD
Retrocopy NQQTEDLPAE<NEATKTEEKPTSDEAGEKEAKSD

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	0.11 RPM	38.63 RPM
SRP051959_heart	0.35 RPM	18.86 RPM
SRP051959_kidney	0.20 RPM	49.03 RPM
SRP051959_liver	0.15 RPM	33.12 RPM
SRP051959_lung	0.33 RPM	40.93 RPM
SRP051959_lymph_node	0.11 RPM	73.12 RPM
SRP051959_skeletal_muscle	0.07 RPM	6.46 RPM
SRP051959_spleen	0.23 RPM	39.47 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2018 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2018 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2018 has 0 orthologous retrocopies within eutheria group .

---

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,