RetrogeneDB ID: retro_cjac_1090

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:39159408..39160544(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000011064
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STK25
• Ensembl ID: ENSCJAG00000006066
• Aliases: None
• Description: None

Sequence

>retro_cjac_1090
ATGGCTCATCTCTGGGGATTTGCCAACCAGCACTCTCGAGTGGATCCGGAGGAGCTCCTCACCAAGCTCGACCGCATTGT
CAAGGGTTCGTTTGGGGAGGTCTACAAGGGCATCATAACCACACCAAGGAGGTGGTGGCCATCAAGATCATCGACCTGGA
GGAGGCTGAGGATGAGATTGAGGACATCAAGCAGGAGATCACCATGCTCAGCCAGTGTGACAGCCCCTATATCACCCGCT
ACTTCGGCTCCTACCTGAAGAGCACCAAGCTATGGATCATCATGGAGTACCTGGGTGGCGGCTCTGCGCTGGACTTGCTG
AAACCTGGCCCCTTGGAGGAGACTTACATTGCCACGATCCTGCGGGAGATTCTGAAGGGCCTGGATTATCTGCACTCTGA
GCGCAAGATCCACCGAGACATCAAAGCTGCCAACGTGCTGCTCTCAGAGCAGGGGGGATGTGAAGCTGGCGGACTTTGGG
GTGACCAGGCAGCTCACAGACACGCAGATCAAGAGGAACATGTTTGTGGGCACCCACTTCTGGATGGCGCCTGAGGTCAT
CAAGCAGTCCGCCTACGACTTCAAGGCCGACATCTGGTCTCTGGGGATCACGGCCATAGTGCTGGCCAAGGGGGAGCCTC
CAAACTCTGACCTCCACCCCATAGGCGTCCTGTTCCTGATTCCCAAGAACAGCCCACCCACCTTGGAGGGCCAACACAGC
AAGCCCTTCAAGGAGTTCGTGGAGGCCTGCCTCAACAAGAACCCCCGATTCCGGCCCACGGCCAAGGAGCTCCTGAAGCA
CAAGTTCATCACACGCTACACCAAGACCTCCCTCCTCATGGAGCTCATTAACCGCTATAAGCGCTGGAAGTCTGAGGGGC
ATGGCGAAGAGTCCAGCTCTGAGTACTCGGACATTGATGGAGAGGCGGAGGACGGGGAGCAGGGCCCGATCTGGACATTC
CCCCGCACCATCCAAGTCCACACAGCAAGCTTCACAAGGGGATGGCCCTGCACGGCTCACAGAAGCCCGTGGAGCCCGTC
AAGAGGCAGCCAAGGTCCCAGTGCCTGTCCACGCTGGTCAGGCCGATCTTCGGAGAGCTCAGAGAGAAGCACAAGCAGAG
CGGCGGGAGCGTGGGC

Alignment

ORF - retro_cjac_1090 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAHLRGFANQHSRVDPEELFTKLDRIGKGSFGEVYKGI-DNHTKEVVAIKIIDLEEAEDEIEDIQQEITV
          MAHL.GFANQHSRVDPEEL.TKLDRI.KGSFGEVYKGI..NHTKEVVAIKIIDLEEAEDEIEDI.QEIT.
Retrocopy MAHLWGFANQHSRVDPEELLTKLDRIVKGSFGEVYKGI<HNHTKEVVAIKIIDLEEAEDEIEDIKQEITM

Parental  LSQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHR
          LSQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHR
Retrocopy LSQCDSPYITRYFGSYLKSTKLWIIMEYLGGGSALDLLKPGPLEETYIATILREILKGLDYLHSERKIHR

Parental  DIKAANVLLSEQG-DVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDFKADIWSLGITAIEL
          DIKAANVLLSEQG.DVKLADFGV..QLTDTQIKRN.FVGT.FWMAPEVIKQSAYDFKADIWSLGITAI.L
Retrocopy DIKAANVLLSEQG>DVKLADFGVTRQLTDTQIKRNMFVGTHFWMAPEVIKQSAYDFKADIWSLGITAIVL

Parental  AKGEPPNSDLHPMRVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKDPRFRPTAKELLKHKFITRYTKKTS
          AKGEPPNSDLHP..VLFLIPKNSPPTLEGQHSKPFKEFVEACLNK.PRFRPTAKELLKHKFITRYT.KTS
Retrocopy AKGEPPNSDLHPIGVLFLIPKNSPPTLEGQHSKPFKEFVEACLNKNPRFRPTAKELLKHKFITRYT-KTS

Parental  FLTELIDRYKRWKSEGHGEESSSEDSDLDGEAEDGEQGPIWTFPPTIRPSPHSKLHKGTALHGSQKPVEP
          .L.ELI.RYKRWKSEGHGEESSSE.SD.DGEAEDGEQGPIWTFP.TI.....S....G........P..P
Retrocopy LLMELINRYKRWKSEGHGEESSSEYSDIDGEAEDGEQGPIWTFPRTIQVHTAS-FTRGWPCTAHRSPWSP

Parental  -VKRQPRSQCLSTLVRPVFGELKEKHKQSGGSVG
          .VKRQPRSQCLSTLVRP.FGEL.EKHKQSGGSVG
Retrocopy <VKRQPRSQCLSTLVRPIFGELREKHKQSGGSVG

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	13.80 RPM
SRP051959_heart	0.49 RPM	20.26 RPM
SRP051959_kidney	0.35 RPM	21.50 RPM
SRP051959_liver	0.39 RPM	16.87 RPM
SRP051959_lung	0.37 RPM	20.29 RPM
SRP051959_lymph_node	0.46 RPM	21.16 RPM
SRP051959_skeletal_muscle	0.55 RPM	23.89 RPM
SRP051959_spleen	0.46 RPM	19.81 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1090 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1090 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1090 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004508	1 retrocopy	retro_cjac_4221,
Callithrix jacchus	ENSCJAG00000006066	1 retrocopy	retro_cjac_1090 ,
Gorilla gorilla	ENSGGOG00000004267	1 retrocopy	retro_ggor_956,
Pongo abelii	ENSPPYG00000025879	5 retrocopies	retro_pabe_1082, retro_pabe_1697, retro_pabe_3581, retro_pabe_3584, retro_pabe_683,