RetrogeneDB ID: retro_cjac_266

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: X:79305649..79306414(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023314
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PTPLA
• Ensembl ID: ENSCJAG00000008663
• Aliases: None
• Description: protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A [Source:HGNC Symbol;Acc:9639]

Sequence

>retro_cjac_266
ATGGCGGCAGCGTCGGCTACTGCAGTGGCGAAGGGGAATGGGGCTGGCAGTGGCCGGGCTGGGGCTGGGGACGCCAGCGG
CACGCAGAAGAAGAAGGGCCTGGGGCCTCTGGTCACGGCATACCTGGTCATCTACAATGAGGTGATGACAGCAGGGTGGC
TGGTTATAGCGGTTGGTCAGGTCCGAGCATACCTGGCTAAGGGTAGCTACCATAGCCTTTATTATTCAATTGAAAAGCCT
TTGAAATTCTTTCAAACTGGAGCCTTATTGGAGGTTTTACATTGTGCTATAGGAATTGTTCCATCTTCTGTTGTCCTGAC
TTCATTCCAGGTGATGTCAAGAGTTTTTCTAATATGGGCAGTAACACACAGCGTCAAAGAGGTACAGACTGAAGACAGTG
TCCTCCTGTTTGTTATTGCCTGGACGATCACGGAAATCATCCGTTACTCCTTTTATACATTCAGTCTATTAAACCATCTG
CCTTACCTCATCAAATGGGCCAGGTACACACTTTTGATTGTGCTGTACCCAATGGGAGTGTCAGGAGAACTGCTCACAAT
ATACGCAGCTCTGCCCTTTGTCAGACAGGCTGGCCTGTATTCCATTAGTTTACCCAACAAATACAATTTCTCTTTTGACT
ACTATGCATTCCTGATTCTAATAATGATCTCCTACATTCCAGTTTTTCCCCAGTTATACTTCCACATGATACACCAGAGA
AGAAAGGTCCTCTCTCATACTGAAGAACACAAGAGATTTGAATAA

Alignment

ORF - retro_cjac_266 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.32 %
• Parental protein coverage: 83.45 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AATMASSDEDGTNGGTSEAGE-DREAPGKRRRLGWLATTWLTFYNIAMTAGWLVLAIAMVRFYMEKGTHR
          AA..A.....G...G...AG..D.....K...LG.L.T..L..YN..MTAGWLV.A...VR.Y..KG...
Retrocopy AAASATAVAKGNGAGSGRAGAGDASGTQKKKGLGPLVTAYLVIYNEVMTAGWLVIAVGQVRAYLAKGSYH

Parental  GLYKSIQKTLKFFQTFALLEIIHCLIGIVPTSVLVTGVQVSSRIFMVWLITHSIKPIQNEESVVLFLVAW
          .LY.SI.K.LKFFQT.ALLE..HC.IGIVP.SV..T..QV.SR.F..W..THS.K..Q.E.SV.LF..AW
Retrocopy SLYYSIEKPLKFFQTGALLEVLHCAIGIVPSSVVLTSFQVMSRVFLIWAVTHSVKEVQTEDSVLLFVIAW

Parental  TVTEITRYSFYTFSLLDHLPYFIKWARYNFFIILYPVGVAGELLTIYAALPYVKKTGMFSIRLPNKYNVS
          T.TEI.RYSFYTFSLL.HLPY.IKWARY...I.LYP.GV.GELLTIYAALP.V...G..SI.LPNKYN.S
Retrocopy TITEIIRYSFYTFSLLNHLPYLIKWARYTLLIVLYPMGVSGELLTIYAALPFVRQAGLYSISLPNKYNFS

Parental  FDYYYFLLITMASYIPLFPQLYFHMLRQRRKVL
          FDYY.FL...M.SYIP.FPQLYFHM..QRRKVL
Retrocopy FDYYAFLILIMISYIPVFPQLYFHMIHQRRKVL

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	1.91 RPM	1.55 RPM
SRP051959_heart	0.72 RPM	13.45 RPM
SRP051959_kidney	2.88 RPM	2.33 RPM
SRP051959_liver	3.94 RPM	3.12 RPM
SRP051959_lung	1.14 RPM	2.78 RPM
SRP051959_lymph_node	1.00 RPM	1.07 RPM
SRP051959_skeletal_muscle	0.33 RPM	6.66 RPM
SRP051959_spleen	0.57 RPM	2.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_266 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_266 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_266 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008663	1 retrocopy	retro_cjac_266 ,
Mus musculus	ENSMUSG00000063275	1 retrocopy	retro_mmus_2120,