RetrogeneDB ID: retro_cjac_2560

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:115033500..115034128(+)
• Located in intron of: ENSCJAG00000000333

Retrocopy information

• Ensembl ID: ENSCJAG00000000354
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SARNP
• Ensembl ID: ENSCJAG00000007853
• Aliases: None
• Description: SAP domain containing ribonucleoprotein [Source:HGNC Symbol;Acc:24432]

Sequence

>retro_cjac_2560
ATGGCGACCGAGACGGTGGAGCTCCATAAGCTGAAGCTTGCTGAACTAAAGCAAGGATGTCTTGCTCGTGCTTTGGAGAC
CAAGGGAATAAAGCAAGATCTTATCCACAGACTCCAGGCATATCTTGAAGAACATGCTGAAGAGGAGGCAAATGAAGAAG
ATGTACTGGGAGATGAAACAGAGGAAGAAGAAACAAAGCCTATAGAGCTCCCTGTCAGAAGAAGAACCCCCTGAAAAAAC
TGTTGATGTGGCAGCAGAGAAGAAAGTGGTAAAAATTACATCTGAAATACCACAGACTGACAGAATGCAGAAGAGGGCCG
AACGATTCAATGTACCTGTGAGCTTGGAGAGTAAGAAAGCTGCTCGGGCAGCTAGGTTTGGGATTTCTTCCGTTCCAACA
AAAGGTCTGTCGTCTGATAACAAACCTATGGTTAACTTGGATAAGCTGAAGGAAGGAGCTCAAAGATTTGGTTTGAATGT
CTCTTCAATCTCCAGAAAGTCTGAAGATGATGAGAAACTGAAAAAGAGGAAGGAACGATTTGGGATTGTCACAAGTTCAG
CTGGAAGTGGAACCACAGAGGATACAGAGGCAAAGAAGAGGAAAAGAGCAAAGCGCTTTGGGATTGCC

Alignment

ORF - retro_cjac_2560 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATETVELHKLKLAELKQECLARGLETKGIKQDLIHRLQAYLEEHAEEEANEEDVLGDETEEE-ETKPIE
          MATETVELHKLKLAELKQ.CLAR.LETKGIKQDLIHRLQAYLEEHA.EE...E........EE.......
Retrocopy MATETVELHKLKLAELKQGCLARALETKGIKQDLIHRLQAYLEEHA-EEEANEEDVLGDETEE>KKQSL*

Parental  LPVKEEEPPEKTVDVAAEKKVVKITSEIPQTERMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLPS
          ....EEEPPEKTVDVAAEKKVVKITSEIPQT.RMQKRAERFNVPVSLESKKAARAARFGISSVPTKGL.S
Retrocopy SSLSEEEPPEKTVDVAAEKKVVKITSEIPQTDRMQKRAERFNVPVSLESKKAARAARFGISSVPTKGLSS

Parental  DNKPMVSLDKLKERAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGSGTTEDTEAKKRKRAERFGI
          DNKPMV.LDKLKE.AQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGSGTTEDTEAKKRKRA.RFGI
Retrocopy DNKPMVNLDKLKEGAQRFGLNVSSISRKSEDDEKLKKRKERFGIVTSSAGSGTTEDTEAKKRKRAKRFGI

Parental  A
          A
Retrocopy A

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	2.02 RPM	14.29 RPM
SRP051959_heart	0.51 RPM	16.98 RPM
SRP051959_kidney	0.55 RPM	18.99 RPM
SRP051959_liver	0.48 RPM	12.97 RPM
SRP051959_lung	0.73 RPM	19.13 RPM
SRP051959_lymph_node	0.64 RPM	21.78 RPM
SRP051959_skeletal_muscle	0.20 RPM	17.54 RPM
SRP051959_spleen	1.07 RPM	21.03 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2560 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2560 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2560 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011769	2 retrocopies	retro_amel_1602, retro_amel_347,
Bos taurus	ENSBTAG00000020662	1 retrocopy	retro_btau_202,
Callithrix jacchus	ENSCJAG00000007853	8 retrocopies	retro_cjac_1070, retro_cjac_1487, retro_cjac_1801, retro_cjac_2439, retro_cjac_2560 , retro_cjac_389, retro_cjac_4139, retro_cjac_731,
Cavia porcellus	ENSCPOG00000011755	1 retrocopy	retro_cpor_1313,
Dipodomys ordii	ENSDORG00000001065	1 retrocopy	retro_dord_80,
Erinaceus europaeus	ENSEEUG00000015176	1 retrocopy	retro_eeur_549,
Homo sapiens	ENSG00000205323	1 retrocopy	retro_hsap_3882,
Gorilla gorilla	ENSGGOG00000013217	2 retrocopies	retro_ggor_2613, retro_ggor_2753,
Loxodonta africana	ENSLAFG00000015053	1 retrocopy	retro_lafr_1024,
Microcebus murinus	ENSMICG00000010902	1 retrocopy	retro_mmur_358,
Monodelphis domestica	ENSMODG00000028949	1 retrocopy	retro_mdom_1909,
Mustela putorius furo	ENSMPUG00000000885	1 retrocopy	retro_mputfur_617,
Mus musculus	ENSMUSG00000078427	1 retrocopy	retro_mmus_54,
Nomascus leucogenys	ENSNLEG00000017599	2 retrocopies	retro_nleu_2779, retro_nleu_569,
Procavia capensis	ENSPCAG00000009477	2 retrocopies	retro_pcap_262, retro_pcap_45,
Pongo abelii	ENSPPYG00000004630	2 retrocopies	retro_pabe_3116, retro_pabe_3358,
Pan troglodytes	ENSPTRG00000029747	2 retrocopies	retro_ptro_2644, retro_ptro_2782,
Rattus norvegicus	ENSRNOG00000030520	2 retrocopies	retro_rnor_1326, retro_rnor_471,