RetrogeneDB ID: retro_cjac_2735

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:74763456..74764219(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SGCE
• Ensembl ID: ENSCJAG00000013426
• Aliases: None
• Description: sarcoglycan, epsilon [Source:HGNC Symbol;Acc:10808]

Sequence

>retro_cjac_2735
TTGTCTAAGGAGAAAAATGTGCTGTGGCCAGAGGCACTAAATGCCATAAACATCATGCTAGTCCTAGATAGGAGCAGCAG
GTTTCTGCTTCCCATTAATGGCCGAAAAGAGGGTGTTTTCATCAGGATTGGTGCTGATGTTCCATTTTCTTCTTGATTAC
AGGATGTTGAAAATCCACAGAATTAACTGAGATGCAGTCAAGAAATGGAGCCTGTAATAACATGTGCTAAAAAATGTTAC
ACTCCATTTTATATTGACTGGTGCAAAATTTCATTTGGTTGATAAAACAAAGCAAGTGGCCACCTATTCGGAAGTGATAA
GTGGAGGGGGAATTGTAGCTGGTGATGGAGAGTATATGCCCTTTTCAAAATGATTATCTGAAAAGCAAACTAGTACTTGG
ATTTCTTAATTATACTAGCTGTGTCCTCAGCAGTAACCCTGGTCTTTTTTCCAGTACTTCTTTACATCATGCACTGTCAA
CAGGAAGGAATAGAAAAGAGAAACATGCAAACACCAGACGTCCAACTGGACCATCACACCGCTATTCAGAAATCTGCCAA
GGAGCTTCAAGGCACATACAAGAGTAGAGAGATAGCATGGCCCCATCAACACTTCTTGTGTTTCACTTGCAACTGGCAAA
ATCACACCTCCACTACACACAAACAACCATGATAGTACTAACACACCATTGGTGCAAATGCAGCATAATTTGCCACATCC
AATTTAGATTCCTCAATAGCAGACTACAAGTAAATATCATCCC

Alignment

ORF - retro_cjac_2735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.39 %
• Parental protein coverage: 64.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LGAVKNVWQPERLNAINITSALDRGGRVPLPINNLKEGVYVMVGADVPFSSCLREVENPQNQLRCSQEME
          L...KNV..PE.LNAINI...LDR..R..LPIN..KEGV....GADVPFSS.L..VENPQN.LRCSQEME
Retrocopy LSKEKNVLWPEALNAINIMLVLDRSSRFLLPINGRKEGVFIRIGADVPFSS*LQDVENPQN*LRCSQEME

Parental  PVITCDKKFRTQFYIDWCKIS-LVDKTKQVSTYQEVIRGEGILPDGGEYKPPSDSLKSRDYYTDF-LITL
          PVITC.KK..T.FYIDWCKIS.LVDKTKQV.TY.EVI.G.GI....GEY.P.S..L......T.......
Retrocopy PVITCAKKCYTPFYIDWCKIS>LVDKTKQVATYSEVISGGGIVAGDGEYMPFSK*LSEKQTSTWI<FLII

Parental  AVPSAVALVLFL-ILAYIMCCRREGVEKRNMQTPDIQLVHHSAIQKSTKELRDMSKNREIAWP-LSTLPV
          ...S......F...L.YIM.C..EG.EKRNMQTPD.QL.HH.AIQKS.KEL....K.REIAWP..STL.V
Retrocopy LAVSSAVTLVFFPVLLYIMHCQQEGIEKRNMQTPDVQLDHHTAIQKSAKELQGTYKSREIAWP<PSTLLV

Parental  FH-PVTGEIIPPLHTDNYDSTNMPLMQTQQNLPHQTQIPQQQTTGKWYP
          FH...TG.I.PPLHT.N.DSTN.PL.Q.Q.NLPH...IPQ.QTT.K..P
Retrocopy FH<LATGKITPPLHTNNHDSTNTPLVQMQHNLPHPI*IPQ*QTTSKYHP

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	0.00 RPM	9.34 RPM
SRP051959_heart	0.07 RPM	12.63 RPM
SRP051959_kidney	0.27 RPM	9.16 RPM
SRP051959_liver	0.00 RPM	2.79 RPM
SRP051959_lung	0.10 RPM	11.22 RPM
SRP051959_lymph_node	0.00 RPM	3.47 RPM
SRP051959_skeletal_muscle	0.02 RPM	4.04 RPM
SRP051959_spleen	0.21 RPM	12.35 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2735 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2735 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2735 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	ENSCJAG00000013426	1 retrocopy	retro_cjac_2735 ,
Tupaia belangeri	ENSTBEG00000008912	1 retrocopy	retro_tbel_2488,