RetrogeneDB ID: retro_cjac_2476

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:133471706..133472450(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000034505
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000009747
• Aliases: None
• Description: None

Sequence

>retro_cjac_2476
ATGGCTGGGATCACCACCATCGAGGTGGTGAAGTGCAAGATCCAGGTTCTGCAGCAGCAGGCAGATGATGCAGAGGAGCG
AGCTGAGCGCCTCCAGAGAGAAGTTGAGGGAGAAAGGCGGGCCCGGGAACAGGCTGAGGCTGAGGTGGCCTCCTTGAACC
GTAGGATCCAGCTGGTTGAAGAGGAGCTGGACCGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCT
GAAAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCGGGCCTTAAAAGATGAAGAGAAGATGGAACT
CCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGATAGGAAGTATGAAGAGGTGGCTCGTAAGTTGG
TGATCATTGAAGGAGACTTGGAACGCACAGAGGAACGAGCTGAGCTGGCAGAGTCCCGTTGCCCAGAGATGGATGAGCCG
ATCAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGACAAATATGAGGA
AGAGATCAAGATTCTTACTGACAAACTCAAGGAGGCAGAGACCCGTGCTGAGTTTGCTGAGAGATCGGTAGCCAAGCTGG
AAAAGACAATTGATGAATTGGAAGATAAACTGAAATGCACCAAAGAGGAGCACCTCTGTACACAAAGGATGCTGGACCAG
ACTCTGCTTGACCTGAATGAGATG

Alignment

ORF - retro_cjac_2476 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.98 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGITTIEAVKRKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
          MAGITTIE.VK.KIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL
Retrocopy MAGITTIEVVKCKIQVLQQQADDAEERAERLQREVEGERRAREQAEAEVASLNRRIQLVEEELDRAQERL

Parental  ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
          ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL
Retrocopy ATALQKLEEAEKAADESERGMKVIENRALKDEEKMELQEIQLKEAKHIAEEADRKYEEVARKLVIIEGDL

Parental  ERTEERAELAESRCREMDEQIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
          ERTEERAELAESRC.EMDE.IRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV
Retrocopy ERTEERAELAESRCPEMDEPIRLMDQNLKCLSAAEEKYSQKEDKYEEEIKILTDKLKEAETRAEFAERSV

Parental  AKLEKTIDDLEDKLKCTKEEHLCTQRMLDQTLLDLNEM
          AKLEKTID.LEDKLKCTKEEHLCTQRMLDQTLLDLNEM
Retrocopy AKLEKTIDELEDKLKCTKEEHLCTQRMLDQTLLDLNEM

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	0.13 RPM	68.16 RPM
SRP051959_heart	0.00 RPM	20.50 RPM
SRP051959_kidney	0.09 RPM	33.86 RPM
SRP051959_liver	0.06 RPM	34.29 RPM
SRP051959_lung	0.18 RPM	91.80 RPM
SRP051959_lymph_node	0.27 RPM	96.96 RPM
SRP051959_skeletal_muscle	0.02 RPM	20.29 RPM
SRP051959_spleen	0.11 RPM	93.74 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2476 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2476 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2476 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
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,
Gorilla gorilla	ENSGGOG00000012668	3 retrocopies	retro_ggor_1239, retro_ggor_1817, retro_ggor_2621,
Nomascus leucogenys	ENSNLEG00000010990	8 retrocopies	retro_nleu_1133, retro_nleu_2050, retro_nleu_2119, retro_nleu_2141, retro_nleu_2387, retro_nleu_2523, retro_nleu_921, retro_nleu_922,
Pongo abelii	ENSPPYG00000000787	2 retrocopies	retro_pabe_1230, retro_pabe_3263,
Rattus norvegicus	ENSRNOG00000017441	1 retrocopy	retro_rnor_1524,
Sus scrofa	ENSSSCG00000006556	3 retrocopies	retro_sscr_318, retro_sscr_604, retro_sscr_781,
Ictidomys tridecemlineatus	ENSSTOG00000023525	6 retrocopies	retro_itri_1453, retro_itri_1558, retro_itri_1837, retro_itri_231, retro_itri_674, retro_itri_709,