RetrogeneDB ID: retro_cjac_125

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:115138547..115140209(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000023111
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GK
• Ensembl ID: ENSCJAG00000007633
• Aliases: None
• Description: None

Sequence

>retro_cjac_125
ATGGCAGCCCCCAAGAAAGCAGTCGCGGGGCCGTTGGTCGGAGCGGTGGTCCAGGGCACCAACTCCACTCGCTTTCTGGT
TTTCAGTTCAAAAACAGCGGAACTACTTAGTCATCACAGAGTGGAATTAACACAAGAGTTCCCAAAAGAAGGTTGGGTGG
AACAAGACCCTAAGGAAATTCTTCAGTCTGTCTATGAGTGTATAGAGAGAACGTGTGAGAAACTTGACGAACTGGATATT
GATATATCCAACATAAAAGCTGTTGGTGTCAGCAATCAGAGGGAAACCACTGTAATCTGGGACAAGTTAACTGGAGAGCC
TCTCTACAATGCTGTGGTGTGGCTGGATCTAAGAACCCAGGCTACCGTTGAGGATCTTAGTAAAAAAATTCCAGGAAATA
ACAACTTCGTCAAGTCTAAGACAGGCCTCCCACTTAGCACTTACTTCAGTGCAGTAAAACTTCGTTGGCTGCTTGACAAT
GTGAGAAACGTCCAAAGGGCTGTTGAAGAAGGTAGAGCTCTTTTTGGTACCATTGATTCATGGCTTATCTGGAGTTTAAC
AGGAGGAGTTAATGGAGGTGTGCATTGTACAGATGTCACAAATGCAAGTAGGACAATGCTTTTTAATATCCATTCTTTGG
AATGGGATAAAGAACTCTGTGACTTTTTTGAAATTCCAATGGGCATTCTTCCAAATGTCTTCAGTTCTTCTGAGATCTAT
GGCATAATTCAAGCTGGGGCCCTGGAAGGTGTGCCAATATCTGGGTGTTTGGGGGACCAATGTGCTGCATTGGTAGGACA
AATGTGCCTCCAAGAAGGACAAGCCAAAAACACCTATGGAACAGGTTGCTTCTTACTATGTAATACAGGTCGTAAATGTG
TGTTTTCTGAACATGGCCTTCTGACCACTGTAGCTTACAAACTAGGCAGAGAGAAACCAGTATATTATGCACTGGAAGGT
TCTGTTGCTATAGCAGGTGCTGTTATTCGTTGGCTAAGAGACAATCTTGGAATTATAGAGACCTCGAGAGACCTTGAAAA
ACTTGCTAAAGAAGTAGGAACTTCTTATGGCTGTTACTTTGTCCCAGCCTTTTCGGGGTTATATGCACCTTACTGGGAGC
CCAGTGCAAGAGGGATACTCTGTGGTCTCACTCAGTTTACCAATAAATGTCATATTGCTTTTGCTGCATTAGAAGCTGTT
TGTTTCCAAACTCGAGAGATTTTGGAAGCCATGAACCGTGACTGTGGAATTCCACTTCGTCATTTGCAGGTAGATGGTGG
AATGACCCACAACAACGTTCTTATGCAACTACAAGCAGATATTCTGCATATTCCAGTAATAAAGCCATTTATGCCTGAAA
CAACTGCACTAGGAGCTGCCATGGCAGCAGGAGCTGCAGAAGGAGTAAATGTTTGGAGTCTTGAACCCCAGGCTTTGTCA
GTTCTCAGGATGGAACGATTTGAACCACAGATCCAGGCCACAGAAAGTGAAATTCGTTATGCTACATGGAAGAAAGCCGT
AATGAAATCAATGGGTTGGGTTACCAGTCAGTCTCCTGAAAGTAGTGATTCTTCTATCTTCTCTAGTCTGCCTTTGGGAT
TTTTTATAGTGAGTAGCATGGTAATACTAATTGGAGCAAGATATATCTCGGGTATACCATAA

Alignment

ORF - retro_cjac_125 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.61 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAASKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILHSVYECIEK
          MAA.KKAV.GPLVGAV.QGT.STRFLVF.SKTAELLSHH.VE..QEFP.EGWVEQDPKEIL.SVYECIE.
Retrocopy MAAPKKAVAGPLVGAVVQGTNSTRFLVFSSKTAELLSHHRVELTQEFPKEGWVEQDPKEILQSVYECIER

Parental  TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKLTGEPLYNAVVWLDLRTQSTVESLSKRIPGNNNFVKSK
          TCEKL..L.IDISNIKA.GVSNQRETTV.WDKLTGEPLYNAVVWLDLRTQ.TVE.LSK.IPGNNNFVKSK
Retrocopy TCEKLDELDIDISNIKAVGVSNQRETTVIWDKLTGEPLYNAVVWLDLRTQATVEDLSKKIPGNNNFVKSK

Parental  TGLPLSTYFSAVKLRWLLDNVRKVQKAVEEKRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
          TGLPLSTYFSAVKLRWLLDNVR.VQ.AVEE.RALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
Retrocopy TGLPLSTYFSAVKLRWLLDNVRNVQRAVEEGRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI

Parental  HSLEWDKQLCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQNGQAKNTYG
          HSLEWDK.LC.FF.IPM.ILPNV.SSSEIYG...AGALEGVPISGCLGDQ.AALVGQMC.Q.GQAKNTYG
Retrocopy HSLEWDKELCDFFEIPMGILPNVFSSSEIYGIIQAGALEGVPISGCLGDQCAALVGQMCLQEGQAKNTYG

Parental  TGCFLLCNTGHKCVFSDHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIESSEEIEKLAK
          TGCFLLCNTG.KCVFS.HGLLTTVAYKLGR.KPVYYALEGSVAIAGAVIRWLRDNLGIIE.S...EKLAK
Retrocopy TGCFLLCNTGRKCVFSEHGLLTTVAYKLGREKPVYYALEGSVAIAGAVIRWLRDNLGIIETSRDLEKLAK

Parental  EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
          EVGTSYGCYFVPAFSGLYAPYWEPSARGI.CGLTQFTNKCHIAFAALEAVCFQTREIL.AMNRDCGIPL.
Retrocopy EVGTSYGCYFVPAFSGLYAPYWEPSARGILCGLTQFTNKCHIAFAALEAVCFQTREILEAMNRDCGIPLR

Parental  HLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
          HLQVDGGMT.N..LMQLQADIL.IPV.KP.MPETTALGAAMAAGAAEGV.VWSLEP..LS...MERFEPQ
Retrocopy HLQVDGGMTHNNVLMQLQADILHIPVIKPFMPETTALGAAMAAGAAEGVNVWSLEPQALSVLRMERFEPQ

Parental  INAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMLIGARYISGIP
          I.A.ESEIRY.TWKKAVMKSMGWVT.QSPES.D.SIF.SLPLGFFIVSSMV.LIGARYISGIP
Retrocopy IQATESEIRYATWKKAVMKSMGWVTSQSPESSDSSIFSSLPLGFFIVSSMVILIGARYISGIP

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	0.00 RPM	23.52 RPM
SRP051959_heart	0.00 RPM	6.44 RPM
SRP051959_kidney	0.00 RPM	47.17 RPM
SRP051959_liver	0.00 RPM	25.47 RPM
SRP051959_lung	0.02 RPM	14.61 RPM
SRP051959_lymph_node	0.00 RPM	4.09 RPM
SRP051959_skeletal_muscle	0.00 RPM	1.92 RPM
SRP051959_spleen	0.00 RPM	8.76 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

12 EST(s) were mapped to retro_cjac_125 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
HX596414	115138528	115139293	100	765	0	765
HX597187	115138534	115139327	99.9	792	1	791
HX610587	115138520	115139336	99.8	814	2	812
HX611612	115138519	115139277	100	758	0	758
HX612095	115138538	115139363	99.7	825	0	824
HX617055	115138541	115139334	100	793	0	793
HX623349	115138514	115139325	100	811	0	811
HX636893	115138490	115139287	100	797	0	797
HX643667	115138538	115139348	100	810	0	810
HX646924	115138538	115139344	100	806	0	806
HX655165	115138541	115139382	99.9	840	1	839
HX660459	115138538	115139341	100	803	0	803

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_125 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_125 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_70
Mus musculus	retro_mmus_119
Rattus norvegicus	retro_rnor_34
Sus scrofa	retro_sscr_59
Canis familiaris	retro_cfam_19

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001924	1 retrocopy	retro_cjac_478,
Callithrix jacchus	ENSCJAG00000007633	3 retrocopies	retro_cjac_125 , retro_cjac_3161, retro_cjac_4035,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Echinops telfairi	ENSETEG00000008279	2 retrocopies	retro_etel_2000, retro_etel_247,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Homo sapiens	ENSG00000198814	4 retrocopies	retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana	ENSLAFG00000007632	1 retrocopy	retro_lafr_30,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Mus musculus	ENSMUSG00000025059	2 retrocopies	retro_mmus_119, retro_mmus_97,
Nomascus leucogenys	ENSNLEG00000010102	2 retrocopies	retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Rattus norvegicus	ENSRNOG00000034116	2 retrocopies	retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Ictidomys tridecemlineatus	ENSSTOG00000008732	1 retrocopy	retro_itri_1436,
Tarsius syrichta	ENSTSYG00000008249	1 retrocopy	retro_tsyr_29,