RetrogeneDB ID: retro_cjac_3206

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 9:35704203..35704652(+)
• Located in intron of: ENSCJAG00000013047

Retrocopy information

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

Parental gene information

• Parental gene symbol: STMN1
• Ensembl ID: ENSCJAG00000009462
• Aliases: None
• Description: stathmin 1 [Source:HGNC Symbol;Acc:6510]

Sequence

>retro_cjac_3206
ATGGCTTCTTCTGATATCCAGGTAAAAGCACTGAAGAAGTGTGCCTCAGGCCGGGCTTTTGATCTGATTCTCAGACCCCA
GTCAAAATAATCTATCCCAGAGTTCCTCATTTCTCCTCCAAAGAAGAAAAATATTTTGCTGGAGGAAACTGAGAATAAAT
TAGAAGCTTCAGAAAAAAGACACAAGCCCTGCAAAGCTGAGATCTTGAAGCAGCTTGCTGAAAACTGAAAGCAGGAGAAA
GAAGTGCTTCAGGAAAAAAAAAAAAAAAAAAAAAAGAACAGCTTCACTAAAACAGAAGAGAAGCTGACCCACAAAATGGA
AGCTAATAAAGAGAACAGGAAGTCGCAAATGGCTACCACACTGGAGTGTTTGCAGAGAAAGATAAGCACATTGAAGAAAT
GCGGAAGAGCAAAGAATCCAGAGACTCTGCTGATGAGAATGAAGCTAAT

Alignment

ORF - retro_cjac_3206 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASSDIQVKELEKRASGQAFELILSPRSKESVPEFPLSPPKKKDLSLEEIQKKLEAAEERRKSHEAEVLK
          MASSDIQVK.L.K.ASG.AF.LIL.P.SK.S.PEF..SPPKKK...LEE...KLEA.E.R.K...AE.LK
Retrocopy MASSDIQVKALKKCASGRAFDLILRPQSK*SIPEFLISPPKKKNILLEETENKLEASEKRHKPCKAEILK

Parental  QLAEKREHEKEVLQ-KAIEENNNFSKMAEEKLTHKMEANKENREAQMAAKLERLR-EKDKHIEEVRKNKE
          QLAE....EKEVLQ........N.....EEKLTHKMEANKENR..QMA..LE.L..EKDKHIEE.RK.KE
Retrocopy QLAEN*KQEKEVLQXXXXXXXXNSFTKTEEKLTHKMEANKENRKSQMATTLECLQ<EKDKHIEEMRKSKE

Parental  SKDPADETEAD
          S.D.ADE.EA.
Retrocopy SRDSADENEAN

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	14.24 RPM
SRP051959_heart	0.33 RPM	5.44 RPM
SRP051959_kidney	0.20 RPM	10.45 RPM
SRP051959_liver	0.17 RPM	1.75 RPM
SRP051959_lung	0.41 RPM	8.04 RPM
SRP051959_lymph_node	0.48 RPM	10.21 RPM
SRP051959_skeletal_muscle	0.15 RPM	3.84 RPM
SRP051959_spleen	0.55 RPM	6.49 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3206 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3206 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3206 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013761	1 retrocopy	retro_btau_247,
Callithrix jacchus	ENSCJAG00000009462	2 retrocopies	retro_cjac_3206 , retro_cjac_474,
Cavia porcellus	ENSCPOG00000011075	1 retrocopy	retro_cpor_1505,
Equus caballus	ENSECAG00000021662	1 retrocopy	retro_ecab_490,
Loxodonta africana	ENSLAFG00000006089	1 retrocopy	retro_lafr_84,
Mustela putorius furo	ENSMPUG00000015774	1 retrocopy	retro_mputfur_1191,
Mus musculus	ENSMUSG00000028832	3 retrocopies	retro_mmus_1660, retro_mmus_2470, retro_mmus_3383,
Oryctolagus cuniculus	ENSOCUG00000006493	1 retrocopy	retro_ocun_56,
Pteropus vampyrus	ENSPVAG00000006344	1 retrocopy	retro_pvam_53,
Rattus norvegicus	ENSRNOG00000016810	4 retrocopies	retro_rnor_1604, retro_rnor_1855, retro_rnor_2048, retro_rnor_765,
Sorex araneus	ENSSARG00000011057	2 retrocopies	retro_sara_271, retro_sara_764,
Sarcophilus harrisii	ENSSHAG00000006382	1 retrocopy	retro_shar_391,
Ictidomys tridecemlineatus	ENSSTOG00000021708	5 retrocopies	retro_itri_1806, retro_itri_1833, retro_itri_554, retro_itri_819, retro_itri_826,