RetrogeneDB ID: retro_cjac_1880

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 2:368006..368504(-)
• Located in intron of: ENSCJAG00000010221

Retrocopy information

• Ensembl ID: ENSCJAG00000015223
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000018571
• Aliases: None
• Description: None

Sequence

>retro_cjac_1880
ATGGCGGCTACCAGTGGAACTGAAGAACCGGTTTCCGGGGAGTTGGTGTCTGTGGCACATGCGCTTTCCCACCCAGCAGA
GTCCTATGGCAACGATCCTGACATTGAGATGGCTTGGGCCATGAGGGCAATGCAGCATGCTGAAGTCTATTACAAGCTGA
TTTCATCAGTTGACCCACAGTTCCTGAAACTCACCAAAGTAGATGACCAAATTTACTCTGAGTTCCGGAAAAATTTTGAG
AAGCTGAAGATAGATGTATTGGACCCAGAAGAACTCAAGTCAGAATCAGCCAAAGAGAAGTGGAGGCCATTCTGCTTAAA
GTTTAATGGGATTGTTGAAGACTTCAACTATGGTACTTTGCTGCAACTAGATTGTTCTCAGGGCTACACTGAAGAAAACA
CCATCTTTGGCCCCAGGATACAATTCTTTGCCATTGAAATTGCTCTGAACCGGGAAGGCTATAACAAAGCTGTTTATATC
AGTGTTCAGGACAAAGAA

Alignment

ORF - retro_cjac_1880 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.14 %
• Parental protein coverage: 71.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAATSGTDEPVSGELVSVAHALSLPAESYGNDPDIEMAWAMRAMQHAEVYYKLISSVDPQFLKLTKVDDQ
          MAATSGT.EPVSGELVSVAHALS.PAESYGNDPDIEMAWAMRAMQHAEVYYKLISSVDPQFLKLTKVDDQ
Retrocopy MAATSGTEEPVSGELVSVAHALSHPAESYGNDPDIEMAWAMRAMQHAEVYYKLISSVDPQFLKLTKVDDQ

Parental  IYSEFRKNFEKLKIDVLDPEELKSESAKEKWRPFCLKFNGIVEDFNYGTLLRLDCSQGYTEENTIFAPRI
          IYSEFRKNFEKLKIDVLDPEELKSESAKEKWRPFCLKFNGIVEDFNYGTLL.LDCSQGYT..........
Retrocopy IYSEFRKNFEKLKIDVLDPEELKSESAKEKWRPFCLKFNGIVEDFNYGTLLQLDCSQGYTXXXXXXXXXX

Parental  QFFAIEIARNREGCNKAVYISVQDKE
          .........NREG.NKAVYISVQDKE
Retrocopy XXXXXXXXXNREGYNKAVYISVQDKE

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	0.31 RPM	2.44 RPM
SRP051959_heart	0.32 RPM	2.70 RPM
SRP051959_kidney	0.13 RPM	3.68 RPM
SRP051959_liver	0.13 RPM	1.73 RPM
SRP051959_lung	0.44 RPM	5.16 RPM
SRP051959_lymph_node	0.64 RPM	5.46 RPM
SRP051959_skeletal_muscle	0.26 RPM	2.66 RPM
SRP051959_spleen	0.40 RPM	4.62 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1880 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1880 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1880 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017228	2 retrocopies	retro_cfam_1588, retro_cfam_944,
Callithrix jacchus	ENSCJAG00000018571	1 retrocopy	retro_cjac_1880 ,
Equus caballus	ENSECAG00000009882	1 retrocopy	retro_ecab_532,
Erinaceus europaeus	ENSEEUG00000001116	1 retrocopy	retro_eeur_377,
Monodelphis domestica	ENSMODG00000009685	2 retrocopies	retro_mdom_1002, retro_mdom_572,
Mus musculus	ENSMUSG00000031226	1 retrocopy	retro_mmus_1569,
Oryctolagus cuniculus	ENSOCUG00000001088	3 retrocopies	retro_ocun_1017, retro_ocun_1402, retro_ocun_595,
Otolemur garnettii	ENSOGAG00000015205	1 retrocopy	retro_ogar_3063,
Rattus norvegicus	ENSRNOG00000002662	3 retrocopies	retro_rnor_1703, retro_rnor_1705, retro_rnor_826,
Sarcophilus harrisii	ENSSHAG00000017872	1 retrocopy	retro_shar_132,
Tupaia belangeri	ENSTBEG00000003411	3 retrocopies	retro_tbel_3448, retro_tbel_494, retro_tbel_979,