RetrogeneDB ID: retro_cjac_3328

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:96381710..96382749(-)
• Located in intron of: ENSCJAG00000014985

Retrocopy information

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

Parental gene information

• Parental gene symbol: HMMR
• Ensembl ID: ENSCJAG00000015371
• Aliases: None
• Description: hyaluronan-mediated motility receptor (RHAMM) [Source:HGNC Symbol;Acc:5012]

Sequence

>retro_cjac_3328
ACAGAAAAACTCTTAGAATATATCCAAGAAATTAGTTGTGCTTCAGACCAAGTGGAAAAATACAATCTAGATATTGCCCA
GTTAGAAGAAAATTTGAAGAAGAATCATGACATTTTAAGGCTTAAGCAGTATATTGAGGAAAATACTGTTATATTATCTA
AACAAGAAGAAGACCTAAATGCAAAAGGTCAGCTGCTTGAAAAAGAAAAAGAAGATCATGTCAACAGGAATAGAGAACAT
AATGAATATCTAAATGCTGAGATGCAAAACCTAAAACAGAAGTTTATTCTTGAACAACAGGAACGTGAAAAGCTTCAACA
AAAGGAATTACAAGAATTATCTTCTAGTCTTCATCAGTTGTGTTCTTTTCAAGAGGAGATGGTTAAAGAGAAGAATCTCT
TTGAGGAAGAATAAAAACAAGCACTGGATGAACTTGATAAATTACAGCAAAAGGAGGAACAATCTGAAAGGCTGGTCAAG
CAATTGGAAGAGGAAACAAAATCTAGAGCTGAAGAATTAAAACTCCTAGAAGAAAAGCTGAAAGGGAAAGAGGCTGAACT
GGAGAAAAGTAGTGCTGCTCATACCCAGGCCACTCTGCTTTTGCAGGAAAAGTTTAACAGTATAGTGCAAAGCCTTGAAG
ATGTTACTGCTCAATTTGAAAGCTATAAAGCATTAACAGCCAGTGAGATAGAAGATCTTAAGCTGCAGAACTCATCATTA
CAGGAAAAAATGGCCAAGGCTGGAAAAAATGCAGAAGATATTCAGGGTGTGGCAACCGAGAGCTCAAGTCAAGAATATGC
AAGGATGCTTCTAGATCTACAGCCCAACTCAGCACTAAAAGAAAGAGAAATTAAAGAAATCAGTTTCTTCTTTTCAAAAA
ATAACTGATTTGCAGAACCAACTCAAGCAACAAGAGGAAGATTTTAGAAAACAACTGGAAGATGAAGCAGCAAGAAAAGC
TGGAAACACAACGGCACAATTAACTGAAGAAATTAACAAGTGGCGTCTCCTTTACAAAGGACTGTATAATAAAATAAAA

Alignment

ORF - retro_cjac_3328 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.32 %
• Parental protein coverage: 56.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SDQVEKYKLDIAQLEENLKEKNHEILSLKQSLEENTVILS-KQVEDLNVKCQLLEKEKEDHVNKNREHNE
          ......Y...I..........N..I..L...L..N..IL..KQ....N....L...E............E
Retrocopy TEKLLEYIQEISCASDQVEKYNLDIAQLEENLKKNHDILRLKQYIEENTVI-LSKQEEDLNAKGQLLEKE

Parental  NLNAEMQNLKHKFILEQQELEKLQQK---ELQVNSLLQQEK--ELSSSLHEKLCSFQEEMVKEKNLFEEE
          .......N..H...L...E...L.QK...E.Q....LQQ....ELSSSLH..LCSFQEEMVKEKNLFEEE
Retrocopy KEDHVNRNREHNEYLNA-EMQNLKQKFILEQQEREKLQQKELQELSSSLHQ-LCSFQEEMVKEKNLFEEE

Parental  LKQALDELDKLQQKEEQSEQLVKQLEEETKSRAEELKLLEEKLKGKEAELEKSSAAHTQATLLLQEKYNS
          .KQALDELDKLQQKEEQSE.LVKQLEEETKSRAEELKLLEEKLKGKEAELEKSSAAHTQATLLLQEK.NS
Retrocopy *KQALDELDKLQQKEEQSERLVKQLEEETKSRAEELKLLEEKLKGKEAELEKSSAAHTQATLLLQEKFNS

Parental  TVQSLEDVTAQFESYKALTASEIEDLKLQNSSLQEKLAKAGKNADDIQGQILATESSNQEYARLLLDLQT
          .VQSLEDVTAQFESYKALTASEIEDLKLQNSSLQEK.AKAGKNA.DIQG...ATESS.QEYAR.LLDLQ.
Retrocopy IVQSLEDVTAQFESYKALTASEIEDLKLQNSSLQEKMAKAGKNAEDIQG--VATESSSQEYARMLLDLQP

Parental  KSALKEREIKEITVSSFQK-ITDLQNQLQQQEEDFRKQLEDEEARKAGKENKMAQLTEEINKWRLLYEEL
          .SALKEREIKEI....F.K.ITDLQNQL.QQEEDFRKQLEDE.ARKAG..N..AQLTEEINKWRLLY..L
Retrocopy NSALKEREIKEISF-FFSK>ITDLQNQLKQQEEDFRKQLEDEAARKAG--NTTAQLTEEINKWRLLYKGL

Parental  YNKVK
          YNK.K
Retrocopy YNKIK

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	0.18 RPM	8.74 RPM
SRP051959_heart	0.28 RPM	4.82 RPM
SRP051959_kidney	0.35 RPM	2.64 RPM
SRP051959_liver	0.11 RPM	2.73 RPM
SRP051959_lung	0.42 RPM	5.60 RPM
SRP051959_lymph_node	0.32 RPM	8.74 RPM
SRP051959_skeletal_muscle	0.11 RPM	4.45 RPM
SRP051959_spleen	0.27 RPM	8.42 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3328 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3328 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3328 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017192	1 retrocopy	retro_cfam_1298,
Callithrix jacchus	ENSCJAG00000015371	1 retrocopy	retro_cjac_3328 ,
Myotis lucifugus	ENSMLUG00000001674	1 retrocopy	retro_mluc_801,