RetrogeneDB ID: retro_cjac_1103

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:59338435..59339190(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKA1
• Ensembl ID: ENSCJAG00000008555
• Aliases: None
• Description: spindle and kinetochore associated complex subunit 1 [Source:HGNC Symbol;Acc:28109]

Sequence

>retro_cjac_1103
TCCTCAGATCTGGAACTATTATGCTCTCATGTTAATGAAAAGATTGGCAATATTAAGAAAACCTTGTCATTAAGAAACTG
TGGCCAGGAACCTACCTTGAAGAATGTATTAAATAAAATAGGAGATGAGATCGCTGTAGCAAATGAACTTCTAAATAAAT
TGGAATTGGAAATTCAGCATCAAGAACAAACCAACAATTCACTCAAAGAACACTGTGAATCTTTTGAAGATTACAAAGAC
ATAGAACATCTTAAAGAAAACATTCCTTCCCATTTGCCACCAAGTAAGAGTCACCCAGAGATGGGTTAAGGGTTCAGATC
TTGACCCTGAAGAACCAGACAAAGCTGTGGACCTGAACCCATAAAGAAGCCCCCCAAAGAACAAACAAGTATTAAGGAAA
TGCCATTTATAACTTGTGATGAGTTCAATGGTGTTCCTTCGTACACGAAATCCCACTGACCTATGGTCAAATTAATCATG
TTACTAAAGAAATCAACAAGGCAGTTATTAGCAAATATACAATCCTATATCAACGAAAAAAGTCTATGAATTCTGTGGCC
AGAAATCTCTATCACAGATTTATTAATGAAGAAACCAAGGATACCAAAGGTTGTTATTCTATAATGGAAGCTGACTTAAA
GGAGTTCACGACTTTGAAAGCTGACAGAAAGTTTCTTGCGATACTTAGTATTTTAAGACACTGCCAGAGGCTATCAGAGG
TCCGAGGGGGAGGACTTACTCCTTATGTTATAACC

Alignment

ORF - retro_cjac_1103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.72 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASDLELLCSHVNEKIANIKKTLSLRNCGQEPTLKTMLNKIGDEIIVVNELLNKLELEIQHQEQTNNSLKE
          .SDLELLCSHVNEKI.NIKKTLSLRNCGQEPTLK..LNKIGDEI.V.NELLNKLELEIQHQEQTNNSLKE
Retrocopy SSDLELLCSHVNEKIGNIKKTLSLRNCGQEPTLKNVLNKIGDEIAVANELLNKLELEIQHQEQTNNSLKE

Parental  LCESLEEDYKDVEHLKENIPSHLL-QVRVTQRCVKGSDLDPEEPDKAVE-PEPIKKPPKEQRSIKEMPFI
          .CES.E.DYKD.EHLKENIPSHL..QVRVTQR.VKGSDLDPEEPDKAV..PEPIKKPPKEQ.SIKEMPFI
Retrocopy HCESFE-DYKDIEHLKENIPSHLP>QVRVTQRWVKGSDLDPEEPDKAVD<PEPIKKPPKEQTSIKEMPFI

Parental  TCDEFNGVPSYMKSR-LTYGQINDVIKEINKAVMSKYKILYQPKKSMNSVARNLYHRFINEETKDTKGHY
          TCDEFNGVPSY.KS..LTYGQIN.V.KEINKAV.SKY.ILYQ.KKSMNSVARNLYHRFINEETKDTKG.Y
Retrocopy TCDEFNGVPSYTKSH<LTYGQINHVTKEINKAVISKYTILYQRKKSMNSVARNLYHRFINEETKDTKGCY

Parental  FIVEADIKEFTTLKVDKKFHVILSILRHCRRLSEVRGGGLTRYVIT
          .I.EAD.KEFTTLK.D.KF..ILSILRHC.RLSEVRGGGLT.YVIT
Retrocopy SIMEADLKEFTTLKADRKFLAILSILRHCQRLSEVRGGGLTPYVIT

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	0.02 RPM	0.82 RPM
SRP051959_heart	0.00 RPM	1.21 RPM
SRP051959_kidney	0.00 RPM	0.18 RPM
SRP051959_liver	0.00 RPM	0.30 RPM
SRP051959_lung	0.00 RPM	1.38 RPM
SRP051959_lymph_node	0.00 RPM	0.53 RPM
SRP051959_skeletal_muscle	0.00 RPM	0.11 RPM
SRP051959_spleen	0.00 RPM	2.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1103 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1103 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1103 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008555	2 retrocopies	retro_cjac_1103 , retro_cjac_875,
Dasypus novemcinctus	ENSDNOG00000000190	1 retrocopy	retro_dnov_1081,
Loxodonta africana	ENSLAFG00000005238	1 retrocopy	retro_lafr_849,
Myotis lucifugus	ENSMLUG00000013388	1 retrocopy	retro_mluc_2127,
Sus scrofa	ENSSSCG00000004518	1 retrocopy	retro_sscr_360,
Tursiops truncatus	ENSTTRG00000015539	1 retrocopy	retro_ttru_1083,