RetrogeneDB ID: retro_cjac_2722

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 6:49442618..49443866(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000006331
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PABPC4
• Ensembl ID: ENSCJAG00000002512
• Aliases: None
• Description: None

Sequence

>retro_cjac_2722
GCCTACGTCAACTTCCAGCAGCCGGCCGATGCTGAGCGGGCTTTGGACACCATGAACTTTGATGTGATTAAGGGAAAGCC
AATCCGCATCATGTGGTCTCAGCGGGATCCCTCTTTGAGAAAATCTGGTGTGGGAAACGTCTTCATTAAGAACCTGGACA
AATCTATAGATAACAAGGCACTTTATGATACTTTTTCTGCTTTTGGAAACATTCTATCCTGCAAGGTGGTACGTGATGAG
AACGGCTCGAAGGGTTATGCCTTTGTCCACTTCGAGACCCAAGAGGCTGCCGACAAGGCCATCGAGAAGATGAATGGCAT
GCTCCTCAATGACCGCAAAGTATTTGTGGGCAGATTCAAGTCTCGCAAAGAGCGGGAAGCCGAGCTTGGAGCCAAAGCCA
AGGAATTCACCAATGTTTATATCAAAAACTTCGGGGAAGAGGTGGATGATCAGAGTCTGAAAGAGCTATTCATTCAGTTT
GGTAAGACCCTGAGTGTCAAGGTGATGAGAGATCCCAACGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTACGAAAAACA
CGAGGATGCCAATAAGGCTGTGGAAGAGATGAATGGAAAAGAAATAAGTGGGAAAATCATATTGGTAGGCCATGCACAAA
AGAAAGTAGAACGGCAGGCAGAGTTAAAATGGAAATTTGAGCAGTTGAAACAGGAAAGAATTAGTCGATACCAGGGGGTG
AATCTCTACATTAAGAACTTGGATGATACTATTGATGATGAGAAATTAAGGAAAGAGTTTTCTCCTTTTGGATCAATTAC
CAGTGCTAAGGTAATGTTGGAAGATGGAAGAAGCAAAGGGTTTGACTTCATCTGCTTCTCGTCTCCTGAAGAGGCAACCA
AAGCAGTCACTGAGATGAATGGATGCATTGTGGGTTCCAAGCCCCTGTATGTTGCCCTGGCCCAGAGGAAGGAAGAGAGA
AAGGCTCACCTGACCAACCAGTATATGCAACGAGTGGCTGGAATGAGAGCACTTCCTGCCAATGCCATCTTAAATCAGTT
CCAGCCAGCAGTGGGTGGCTACTTCGTGCCAGCAGTCCCACAGGTTCAGGGAAGGCCTCCATATTATACACCTAACCAGT
TAGCACAGATGAGGCCTAATCCACGCTGGCAGCAAGGTGGGAGACCTCAAGGCTGTCAAGGAATGCCAAGTGCTATATGC
CAGTCTGGGCCTTGTCCAATTCTTCGCCATCTGGCTCCAACTGGGTCT

Alignment

ORF - retro_cjac_2722 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.7 %
• Parental protein coverage: 63.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AYVNFQQPADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGN
          AYVNFQQPADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGN
Retrocopy AYVNFQQPADAERALDTMNFDVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGN

Parental  ILSCKVVCDENGSKGYAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVY
          ILSCKVV.DENGSKGYAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVY
Retrocopy ILSCKVVRDENGSKGYAFVHFETQEAADKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVY

Parental  IKNFGEEVDDESLKELFIQFGKTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIIFVG
          IKNFGEEVDD.SLKELFIQFGKTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKII.VG
Retrocopy IKNFGEEVDDQSLKELFIQFGKTLSVKVMRDPNGKSKGFGFVSYEKHEDANKAVEEMNGKEISGKIILVG

Parental  RAQKKVERQAELKRKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKG
          .AQKKVERQAELK.KFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKG
Retrocopy HAQKKVERQAELKWKFEQLKQERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKG

Parental  FGFVCFSSPEEATKAVTEMNGRIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPA
          F.F.CFSSPEEATKAVTEMNG.IVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPA
Retrocopy FDFICFSSPEEATKAVTEMNGCIVGSKPLYVALAQRKEERKAHLTNQYMQRVAGMRALPANAILNQFQPA

Parental  AGGYFVPAVPQSYTAQGRPPYYTPNQLAQMRPNPRWQQGGRPQGFQGMPSAIRQSGPRPTLRHLAPTGN
          .GGYFVPAVPQ....QGRPPYYTPNQLAQMRPNPRWQQGGRPQG.QGMPSAI.QSGP.P.LRHLAPTG.
Retrocopy VGGYFVPAVPQ---VQGRPPYYTPNQLAQMRPNPRWQQGGRPQGCQGMPSAICQSGPCPILRHLAPTGS

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	0.51 RPM	17.20 RPM
SRP051959_heart	1.16 RPM	36.68 RPM
SRP051959_kidney	0.44 RPM	23.67 RPM
SRP051959_liver	1.04 RPM	26.92 RPM
SRP051959_lung	0.63 RPM	22.81 RPM
SRP051959_lymph_node	0.82 RPM	20.73 RPM
SRP051959_skeletal_muscle	2.58 RPM	63.59 RPM
SRP051959_spleen	0.90 RPM	30.69 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2722 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2722 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2722 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 48 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011535	2 retrocopies	retro_amel_107, retro_amel_676,
Callithrix jacchus	ENSCJAG00000002512	3 retrocopies	retro_cjac_214, retro_cjac_2722 , retro_cjac_284,
Callithrix jacchus	ENSCJAG00000010803	1 retrocopy	retro_cjac_1022,
Callithrix jacchus	ENSCJAG00000014861	1 retrocopy	retro_cjac_1040,
Callithrix jacchus	ENSCJAG00000015833	5 retrocopies	retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus	ENSCPOG00000009552	2 retrocopies	retro_cpor_1330, retro_cpor_77,
Felis catus	ENSFCAG00000015254	2 retrocopies	retro_fcat_116, retro_fcat_545,
Homo sapiens	ENSG00000090621	2 retrocopies	retro_hsap_109, retro_hsap_74,
Gorilla gorilla	ENSGGOG00000004002	3 retrocopies	retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Microcebus murinus	ENSMICG00000016633	1 retrocopy	retro_mmur_675,
Macaca mulatta	ENSMMUG00000007497	1 retrocopy	retro_mmul_178,
Monodelphis domestica	ENSMODG00000017657	2 retrocopies	retro_mdom_1090, retro_mdom_1805,
Mustela putorius furo	ENSMPUG00000014414	2 retrocopies	retro_mputfur_152, retro_mputfur_546,
Mus musculus	ENSMUSG00000011257	7 retrocopies	retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys	ENSNLEG00000011928	2 retrocopies	retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus	ENSOCUG00000000562	2 retrocopies	retro_ocun_153, retro_ocun_792,
Otolemur garnettii	ENSOGAG00000004067	1 retrocopy	retro_ogar_71,
Ochotona princeps	ENSOPRG00000011984	1 retrocopy	retro_opri_1133,
Pongo abelii	ENSPPYG00000001506	2 retrocopies	retro_pabe_190, retro_pabe_2563,
Pan troglodytes	ENSPTRG00000000573	3 retrocopies	retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus	ENSRNOG00000015642	2 retrocopies	retro_rnor_175, retro_rnor_92,
Sarcophilus harrisii	ENSSHAG00000018139	1 retrocopy	retro_shar_823,