RetrogeneDB ID: retro_cjac_3837

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL284935.1:1510..2216(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000009411
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TMEM127
• Ensembl ID: ENSCJAG00000007489
• Aliases: None
• Description: transmembrane protein 127 [Source:HGNC Symbol;Acc:26038]

Sequence

>retro_cjac_3837
TACGCCCCCGGAGGCGCAGGGCCACCTGGCGGGCGCCGGCGGAGAAGCCCGGGAAGCAGCGCTCTGCCCAAGCAGCCGGC
GCACAGCCTGGCCTCTGCCCTGCCTGGCGCCCTGTCCATCACGGTGCTGTGCTTTGCCCTTGCCGAGCGCTCCTGGTTGC
CCATCCACGGAGGCACCTGTTCTGGCCAGGAGCTGGGGGTCTCCGACGTATTGGGCTGTGTGCACCTGGACCTGCTGAAA
GATTTCTGCATGAATCCCCAGACCGTGCTGCTCCTGCGGGTCATCTGCTGCCTTCTGCCTCCTGGAAATCCTGTGTTGTC
TCTCCGCTTTCCTTCTGGATGTCTTTGGTCCCAAGCATCCCGACCTGAAGATCACCCATCGCTATGCCTTCGCCCATATC
CTCACTGTCCTGCAGTGTGCCACTGTCACTGGCGTTTTTTATTGGGCTTCTGAACTCATCCTGGCCCAGCAGCAGCAGCA
GCATAAGTACCATGGATCCCAGGTCTATGTCACCTTCGCTGTTAGCTTCTACCTGGTGGCAGGAGCTGGTGGAGCCTCAA
TCCTGGCCACAGCAGCCAACCTCCTTCACCACTACCCCATAGAGAAAGAGAAGCAGGCGCTGGAGCTGCTCTCTGAGATG
GAGAACGGGCCCTACCCGGCGGAATATGAGGTCATCAACCAGTTCCAGCCACCTCCTGCCTACACA

Alignment

ORF - retro_cjac_3837 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.76 %
• Parental protein coverage: 99.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YAPGGAGLPGGRRRRSPGGSALPKQPERSLASALPGALSITALCTALAEPAWLHIHGGTCSRQELGVSDV
          YAPGGAG.PGGRRRRSPG.SALPKQP..SLASALPGALSIT.LC.ALAE..WL.IHGGTCS.QELGVSDV
Retrocopy YAPGGAGPPGGRRRRSPGSSALPKQPAHSLASALPGALSITVLCFALAERSWLPIHGGTCSGQELGVSDV

Parental  LGYVHPDLLKDFCMNPQTVLLLRVI-AAFCFLGILCSLSAFLLDVFGPKHPALKITRRYAFAHILTVLQC
          LG.VH.DLLKDFCMNPQTVLLLRVI.AAFC.L.ILC.LSAFLLDVFGPKHP.LKIT.RYAFAHILTVLQC
Retrocopy LGCVHLDLLKDFCMNPQTVLLLRVI>AAFCLLEILCCLSAFLLDVFGPKHPDLKITHRYAFAHILTVLQC

Parental  ATVIGFSYWASELILAQQQQHKKYHGSQVYVTFAVSFYLVAGAGGASILATAANLLRHYPTEEEEQALEL
          ATV.G..YWASELILAQQQQ..KYHGSQVYVTFAVSFYLVAGAGGASILATAANLL.HYP.E.E.QALEL
Retrocopy ATVTGVFYWASELILAQQQQQHKYHGSQVYVTFAVSFYLVAGAGGASILATAANLLHHYPIEKEKQALEL

Parental  LSEMEENEPYPAEYEVINQFQPPPAYT
          LSEM.EN.PYPAEYEVINQFQPPPAYT
Retrocopy LSEM-ENGPYPAEYEVINQFQPPPAYT

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	13.42 RPM
SRP051959_heart	0.02 RPM	9.66 RPM
SRP051959_kidney	0.00 RPM	10.36 RPM
SRP051959_liver	0.00 RPM	6.76 RPM
SRP051959_lung	0.00 RPM	11.26 RPM
SRP051959_lymph_node	0.00 RPM	10.36 RPM
SRP051959_skeletal_muscle	0.00 RPM	7.91 RPM
SRP051959_spleen	0.02 RPM	9.01 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3837 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3837 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3837 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007489	1 retrocopy	retro_cjac_3837 ,