RetrogeneDB ID: retro_cjac_2280

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 3:137157358..137158321(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000018072
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000002214
• Aliases: None
• Description: None

Sequence

>retro_cjac_2280
ATGGTGCCGAAGCCAGACCCGAAGCCTAAATTCCAGGAGGGTGAGCGAGTGCGGTGCTTTCATGGGCCTCTTCTGTATGA
AGCAAAGTGTGTAAAGGTTGCCTTAAAGGACAAACAAGTGAAATACTTCATACATTACAGTGGTTGAATAAAAATTGGGA
TGAGTGGGTTCCGGAGAGCCAGGTACTCAAATATGTGGACACCAATTTGCAGAAACAGCGAGAACTTCAAAAAGCCAATC
AGGAGCAGTATGCAGAGGGGAAGATGAGAGGGGCTGCCCCAGGAAAGAAGACGTCTGGTCTGCAACAGAAAAATGTTGAA
GTGAAAACAAAAAAGAACAAACAGAAAACACCGGGACATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGCCTCCTCG
GAAAAGGGCCCGGGTAGATCCTACTGTTGAAAATGAAACATTCATGAACAGAGTTGAAGTTAAAGTAAAGATTCCTGAAG
AACTAAAATCATGGCTTGTTGATGACTGGGACTTAATTACCAGGCAAAAGCAGCTCTTTTATCTTCCTCTCAGGAAGAAT
GTAGATTCCATTCTTGAGGATTATGCAAATGACAATAAATCTCGTGGAAACACAGATAATAAGGAGTATGCGGTTAATGA
AGTTGTGGCAGGGACAAAAGAATACTTCAATGTAATGTTGGGTACCCAGCTACTCTACAAATTTGAGAGAACACAGTATG
CTGAAATTCTTGCAGATCACCCTGATGCATCCATGTCCCAGGCGTTATGGGGCGCCACATCTACTGAGGCTATTTGTACG
AATTGGAGCAATGTTGGCCTATACACCTCTGGATGAGAAGAGCCTTGCTTTATTACTGAATTATCTTCACGATTTCCTAA
AGTACGTAGCAAAGAAGTCAGCAACTTTATTTAGTGCCCGTGATTATGAAGTGGCTCCTCCTGAGTACCATCGGAAAGCT
GTG

Alignment

ORF - retro_cjac_2280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.92 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSG-WNKNWDEWVPESRVLKYVDTN
          M.PK.DPKPKFQEGERV.CFHGPLLYEAKCVKVA.KDKQVKYFIHYSG..NKNWDEWVPES.VLKYVDTN
Retrocopy MVPKPDPKPKFQEGERVRCFHGPLLYEAKCVKVALKDKQVKYFIHYSG<LNKNWDEWVPESQVLKYVDTN

Parental  LQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRAR
          LQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPG.GDGGSTSETPQPPRK.RAR
Retrocopy LQKQRELQKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGHGDGGSTSETPQPPRK-RAR

Parental  VDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDN
          VDPTVENE.TFMNRVEVKVKIPEELK.WLVDDWDLITRQKQLFYLP..KNVDSILEDYAN..KSRGNTDN
Retrocopy VDPTVENE-TFMNRVEVKVKIPEELKSWLVDDWDLITRQKQLFYLPLRKNVDSILEDYANDNKSRGNTDN

Parental  KEYAVNEVVAGIKEYFNVMLGTQLLYKFERPQYAEILADHPDAPMSQV-YGAPHLLRLFVRIGAMLAYTP
          KEYAVNEVVAG.KEYFNVMLGTQLLYKFER.QYAEILADHPDA.MSQ..YGAPHLLRLFVRIGAMLAYTP
Retrocopy KEYAVNEVVAGTKEYFNVMLGTQLLYKFERTQYAEILADHPDASMSQA>YGAPHLLRLFVRIGAMLAYTP

Parental  LDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
          LDEKSLALLLNYLHDFLKY.AK.SATLFSA.DYEVAPPEYHRKAV
Retrocopy LDEKSLALLLNYLHDFLKYVAKKSATLFSARDYEVAPPEYHRKAV

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	0.20 RPM	41.34 RPM
SRP051959_heart	0.28 RPM	63.99 RPM
SRP051959_kidney	0.60 RPM	72.19 RPM
SRP051959_liver	0.28 RPM	40.90 RPM
SRP051959_lung	0.16 RPM	58.89 RPM
SRP051959_lymph_node	0.25 RPM	43.58 RPM
SRP051959_skeletal_muscle	0.44 RPM	34.22 RPM
SRP051959_spleen	0.34 RPM	52.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2280 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2280 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 28 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012344	1 retrocopy	retro_amel_124,
Bos taurus	ENSBTAG00000010988	1 retrocopy	retro_btau_137,
Canis familiaris	ENSCAFG00000014113	1 retrocopy	retro_cfam_20,
Callithrix jacchus	ENSCJAG00000002214	5 retrocopies	retro_cjac_2113, retro_cjac_2280 , retro_cjac_2574, retro_cjac_3026, retro_cjac_3179,
Cavia porcellus	ENSCPOG00000003778	3 retrocopies	retro_cpor_114, retro_cpor_1409, retro_cpor_915,
Equus caballus	ENSECAG00000008091	1 retrocopy	retro_ecab_62,
Felis catus	ENSFCAG00000012197	1 retrocopy	retro_fcat_75,
Homo sapiens	ENSG00000185787	3 retrocopies	retro_hsap_309, retro_hsap_3125, retro_hsap_850,
Gorilla gorilla	ENSGGOG00000016826	3 retrocopies	retro_ggor_125, retro_ggor_2141, retro_ggor_694,
Loxodonta africana	ENSLAFG00000009851	1 retrocopy	retro_lafr_62,
Myotis lucifugus	ENSMLUG00000001756	1 retrocopy	retro_mluc_324,
Macaca mulatta	ENSMMUG00000022926	1 retrocopy	retro_mmul_1064,
Monodelphis domestica	ENSMODG00000011517	2 retrocopies	retro_mdom_150, retro_mdom_158,
Mustela putorius furo	ENSMPUG00000015429	1 retrocopy	retro_mputfur_180,
Mus musculus	ENSMUSG00000062270	9 retrocopies	retro_mmus_1454, retro_mmus_1697, retro_mmus_176, retro_mmus_1771, retro_mmus_1825, retro_mmus_1833, retro_mmus_2500, retro_mmus_2612, retro_mmus_289,
Nomascus leucogenys	ENSNLEG00000008678	3 retrocopies	retro_nleu_417, retro_nleu_445, retro_nleu_51,
Oryctolagus cuniculus	ENSOCUG00000015117	2 retrocopies	retro_ocun_108, retro_ocun_21,
Otolemur garnettii	ENSOGAG00000006047	4 retrocopies	retro_ogar_1594, retro_ogar_2616, retro_ogar_2896, retro_ogar_50,
Pongo abelii	ENSPPYG00000006703	4 retrocopies	retro_pabe_1046, retro_pabe_201, retro_pabe_2581, retro_pabe_695,
Pan troglodytes	ENSPTRG00000007351	3 retrocopies	retro_ptro_2114, retro_ptro_47, retro_ptro_591,
Rattus norvegicus	ENSRNOG00000014410	6 retrocopies	retro_rnor_1076, retro_rnor_2270, retro_rnor_2357, retro_rnor_374, retro_rnor_793, retro_rnor_980,
Sorex araneus	ENSSARG00000004519	1 retrocopy	retro_sara_15,
Sarcophilus harrisii	ENSSHAG00000018402	1 retrocopy	retro_shar_393,
Sus scrofa	ENSSSCG00000001769	1 retrocopy	retro_sscr_93,
Ictidomys tridecemlineatus	ENSSTOG00000013294	3 retrocopies	retro_itri_111, retro_itri_1545, retro_itri_1608,
Tupaia belangeri	ENSTBEG00000001897	8 retrocopies	retro_tbel_1694, retro_tbel_1704, retro_tbel_4638, retro_tbel_518, retro_tbel_550, retro_tbel_69, retro_tbel_753, retro_tbel_76,
Tursiops truncatus	ENSTTRG00000016606	1 retrocopy	retro_ttru_472,
Vicugna pacos	ENSVPAG00000008847	1 retrocopy	retro_vpac_229,