RetrogeneDB ID: retro_cjac_2200

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:166070998..166071723(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033349
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: TPM1
• Ensembl ID: ENSCJAG00000004355
• Aliases: None
• Description: tropomyosin 1 (alpha) [Source:HGNC Symbol;Acc:12010]

Sequence

>retro_cjac_2200
GCCGGCCTCAACTCTCTAGAGACGGTGAAACACAAGATCCAGGCCCTGCAGCAGCAGGCGGACTAGGAGGAAGACCGCGC
GCAGGTCCTGCAGCGGGAGCTGGACTGCGAGCGCGAATGGCGCGAGAAAGCTGAAGGTGATATGGCCGCCCTTAACCGAG
GCATCCAGCTAGTTGAGGAGGAGCTCTACAGGGCTCAGGAACGACCAGCCACAGCCCTGCAGAAGCTGGAGAAGGTGGAA
AAGGCCGCAGATGAGAGTGAGAGAGGAATGAAGGCGATAGAAAACCGGCCATGAAGGATGAGAAGATGGAGATTCAGGAG
ATGCAGCTGAAAGAGGCCAAGCACGTTGCGGGAGAAGCTGACCGCAAACACGAGGAGGTAGCTTGGAATCTGGACGCCCT
GGAGGGTGAGCTGGAGAGGGCAGAGGCATGTGCGGAGCTGTCTGAACTAAAATGTGGCGACCTGGAAGAAGAACTCAAGA
ATGTTACTAACAATCTGAGGTCGCTGGAGGCTGCATCTGAAAAGTATTCTGAAAAGGTAGGCAAGTATGAAGAAGTAATT
AAACTTCTGTCTGACAAACTGAAAGAAGCTGAGACCCGTGCCGAATTTGCAGAGAGAACAGTGGCAAAACTGGAAAAGAC
CCTTGATGACCTGGAAGAGAAACTTGCCCAGGCCAAAGAAGCGAACGTGGGCTTACATCAGACACTGGATCAGACACTAA
ACGAA

Alignment

ORF - retro_cjac_2200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.67 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AGSSSLEAVRRKIRSLQEQADAAEERAGSLQRELDHERKLRETAEADVASLNRRIQLVEEELDRAQERLA
          AG..SLE.V..KI..LQ.QAD..E.RA..LQRELD.ER..RE.AE.D.A.LNR.IQLVEEEL.RAQER.A
Retrocopy AGLNSLETVKHKIQALQQQAD*EEDRAQVLQRELDCEREWREKAEGDMAALNRGIQLVEEELYRAQERPA

Parental  TALQKLEEAEKAADESERGMKVIESR-AQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDL
          TALQKLE..EKAADESERGMK.IE.R.A.KDE.KMEIQE.QLKEAKH.A..ADRK.EEVA..L...E..L
Retrocopy TALQKLEKVEKAADESERGMKAIENR<AMKDE-KMEIQEMQLKEAKHVAGEADRKHEEVAWNLDALEGEL

Parental  ERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLSDKLKEAETRAEFAERSV
          ERAE..AELSE.KC..LEEELK.VTNNL.SLEA..EKYS.K..KYEE.IK.LSDKLKEAETRAEFAER.V
Retrocopy ERAEACAELSELKCGDLEEELKNVTNNLRSLEAASEKYSEKVGKYEEVIKLLSDKLKEAETRAEFAERTV

Parental  TKLEKSIDDLEDQLYQQLEQNRRLTNELKLALNE
          .KLEK..DDLE..L.Q..E.N..L...L...LNE
Retrocopy AKLEKTLDDLEEKLAQAKEANVGLHQTLDQTLNE

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	10.07 RPM	180.61 RPM
SRP051959_heart	3.46 RPM	820.43 RPM
SRP051959_kidney	2.57 RPM	59.77 RPM
SRP051959_liver	0.89 RPM	28.33 RPM
SRP051959_lung	6.43 RPM	84.75 RPM
SRP051959_lymph_node	3.81 RPM	29.06 RPM
SRP051959_skeletal_muscle	1.51 RPM	1671.70 RPM
SRP051959_spleen	5.02 RPM	64.71 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2200 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2200 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2200 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016966	1 retrocopy	retro_cfam_2167,
Choloepus hoffmanni	ENSCHOG00000012788	11 retrocopies	retro_chof_1194, retro_chof_1272, retro_chof_1360, retro_chof_1789, retro_chof_1829, retro_chof_2309, retro_chof_346, retro_chof_399, retro_chof_412, retro_chof_770, retro_chof_967,
Callithrix jacchus	ENSCJAG00000004355	2 retrocopies	retro_cjac_2200 , retro_cjac_691,
Callithrix jacchus	ENSCJAG00000009627	2 retrocopies	retro_cjac_1839, retro_cjac_1894,
Callithrix jacchus	ENSCJAG00000009747	9 retrocopies	retro_cjac_1232, retro_cjac_1509, retro_cjac_1580, retro_cjac_1910, retro_cjac_2476, retro_cjac_3121, retro_cjac_527, retro_cjac_785, retro_cjac_798,
Callithrix jacchus	ENSCJAG00000014135	1 retrocopy	retro_cjac_206,
Macropus eugenii	ENSMEUG00000014581	2 retrocopies	retro_meug_1944, retro_meug_2161,
Pongo abelii	ENSPPYG00000006534	1 retrocopy	retro_pabe_624,
Ictidomys tridecemlineatus	ENSSTOG00000009955	1 retrocopy	retro_itri_166,
Tursiops truncatus	ENSTTRG00000003762	1 retrocopy	retro_ttru_446,
Vicugna pacos	ENSVPAG00000003277	1 retrocopy	retro_vpac_424,