RetrogeneDB ID: retro_cjac_875

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 11:110270156..110270844(+)
• Located in intron of: ENSCJAG00000019962

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_875
TCCTCAGATCTGGAACTGTTATGCTCTCATGTTAATGAAAAGTTTGGCAATATTAAGAAAACCTTGTCATTAAGAAACTG
TGGCCAGGAACCTACCTTGAAGACTATGTTAAATAAAATAGGAGATGAGATCATTGTAGTAAATGAACTTCTAAATAAAT
TGTAATTGGAAATTCAGCATCAAGAACAAACCAATTCACTTAAGGAACTCAGTGAATCCCTTGAAGAAGATTACAAGGAT
GTGTAGAACATCTTAAAGAAAACACTCCTTCCCACGGGCCACAAGTAAGAGTCACCCAGAGATGTGTTAAGGGATCAGAT
CTTGATCCTGAAGAACCAGACAAAGCTGTGGAACCTGAACCCAGAAAGAAGCCCCCCAAATAACAAACAAGTATTAAGGA
AATGCCATTTATACCTTGTGACAAGTTCAATGGTGTGCCTTCGTACATGCAATCCCGCTTAACCTATGGTCAAATTAATG
ATGTTATTAAAGAAATCAACACGGCAGTAATGAGTAAATATAAAATCCTGATCAACCAACAAAGTCTATGAATTCTGTGG
CCAGAAATCTCTATCACAGATTTATTAATGAAGAAACGAAGGATACTGAAGGTCATTATTTTATAGTGGAAGCTGACATA
AAGGAGTTCACGACTTTGAAAGTTGACAAAAAGTTTCATGTGATACTA

Alignment

ORF - retro_cjac_875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.84 %
• Parental protein coverage: 90.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ASDLELLCSHVNEKIANIKKTLSLRNCGQEPTLKTMLNKIGDEIIVVNELLNKLELEIQHQEQTNNSLKE
          .SDLELLCSHVNEK..NIKKTLSLRNCGQEPTLKTMLNKIGDEIIVVNELLNKL.LEIQHQEQT.NSLKE
Retrocopy SSDLELLCSHVNEKFGNIKKTLSLRNCGQEPTLKTMLNKIGDEIIVVNELLNKL*LEIQHQEQT-NSLKE

Parental  LCESLEEDYKDV-EHLKENI-PSHLLQVRVTQRCVKGSDLDPEEPDKAVEPEPIKKPPKEQRSIKEMPFI
          L.ESLEEDYKDV...LK....PSH..QVRVTQRCVKGSDLDPEEPDKAVEPEP.KKPPK.Q.SIKEMPFI
Retrocopy LSESLEEDYKDV*NILKKTL<PSHGPQVRVTQRCVKGSDLDPEEPDKAVEPEPRKKPPK*QTSIKEMPFI

Parental  TCDEFNGVPSYMKSRLTYGQINDVIKEINKAVMSKYKILY-QPKKSMNSVARNLYHRFINEETKDTKGHY
          .CD.FNGVPSYM.SRLTYGQINDVIKEIN.AVMSKYKIL..QP.KSMNSVARNLYHRFINEETKDT.GHY
Retrocopy PCDKFNGVPSYMQSRLTYGQINDVIKEINTAVMSKYKILI<QPTKSMNSVARNLYHRFINEETKDTEGHY

Parental  FIVEADIKEFTTLKVDKKFHVIL
          FIVEADIKEFTTLKVDKKFHVIL
Retrocopy FIVEADIKEFTTLKVDKKFHVIL

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	0.33 RPM	0.82 RPM
SRP051959_heart	0.19 RPM	1.21 RPM
SRP051959_kidney	0.29 RPM	0.18 RPM
SRP051959_liver	0.09 RPM	0.30 RPM
SRP051959_lung	0.52 RPM	1.38 RPM
SRP051959_lymph_node	0.78 RPM	0.53 RPM
SRP051959_skeletal_muscle	0.11 RPM	0.11 RPM
SRP051959_spleen	0.34 RPM	2.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_875 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_875 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_875 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,