RetrogeneDB ID: retro_cjac_2574

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 5:141337975..141338937(+)
• Located in intron of: ENSCJAG00000019447

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

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

Sequence

>retro_cjac_2574
ATGGCGTCGAAGCAGGACCTGAAGCCTAAATTCCAGAAGGGTGAGTGAGTGCTGTGCTTTCATGGGCCTCTTCTGTATGA
AGCAAAGTGTGTAAAGGTTGCCATAAAGGACAAACAAGTGAAATACTTCATACATTACAGTGGTTGGAATAAAAATTGGG
ATGAGTGGGTTCTGGAGAGCCGAGTACTCAAATATGAGGACGCCAATTTGCAGAAACAGTGAGAACTTTAAAAAGCCAAC
CAGGAGCAGTATGCGGAGGGGAAGATGAGAGGGGCTGCCCCAGGACAGAAGTCATCTGGTCTGCAACAGAAAAATGTTGA
CATGAAAACCAAAAAACAAACAGAAAACACCTGGAAATGGAGATGGTGATAGTACCAGTGAGACGACTCAGCCTCCTCGG
AAGAAAAGGGCCCAGGTGGATCCTACTGTTGAAAATGAGGAAACATTCATGAACAGAGTTGAAGTCAAAGTAAAGATTCC
TGAGGAACTAAAACGGTGGCTTGTGGATGACTGTGACTTAATTACCAGGCAAAAGAAGCTCTTTTATCTTCCTGCCAAGA
AGAATGTGGATTCCATTCTTGAGGATTATACAAATTATAAGAAATCTCGTGGAAACACAGATAATAAGGAGTATGCGGTT
AATGAAGTTGTGGCAGGGATAAAAGAATACTTCAGTGTAATGTTGGGACCAGCTACTCTACAAATTTGAGAGACTGCAGT
ATGCTGAAATTCTTGCAGATCACCCTGATGCACCCATGTCCCAGGTGTATGGGGCGCCACATCTGTGATTATTTGTACGA
ATTGGAGCAATGTTGGTCTATACACCTCTGGATGAGAAGAGCCTTGCTTTATTACTGAATTATCTTCACGATTTCCTAAA
GTACCTGGCAAAGAACTCTGCAACTTTGTTTAGTGCCAGTGATTATGAAGTGGTTCCTCCTGAGCACCATCAGAAAGCTG
TG

Alignment

ORF - retro_cjac_2574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAPKQDPKPKFQEGERVLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVPESRVLKYVDTNL
          MA.KQD.KPKFQ.GE.VLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWV.ESRVLKY.D.NL
Retrocopy MASKQDLKPKFQKGE*VLCFHGPLLYEAKCVKVAIKDKQVKYFIHYSGWNKNWDEWVLESRVLKYEDANL

Parental  QKQREL-QKANQEQYAEGKMRGAAPGKKTSGLQQKNVEVKTKKNKQKTPGNGDGGSTSETPQPPRKKRAR
          QKQ.EL..K........G...G............K....K.K.NKQKTPGNGDG.STSET.QPPRKKRA.
Retrocopy QKQ*EL>KKPTRSSMRRGR*EGLPQDRSHLVCNRKMLT*KPK-NKQKTPGNGDGDSTSETTQPPRKKRAQ

Parental  VDPTVENEETFMNRVEVKVKIPEELKPWLVDDWDLITRQKQLFYLPAKKNVDSILEDYANYKKSRGNTDN
          VDPTVENEETFMNRVEVKVKIPEELK.WLVDD.DLITRQK.LFYLPAKKNVDSILEDY.NYKKSRGNTDN
Retrocopy VDPTVENEETFMNRVEVKVKIPEELKRWLVDDCDLITRQKKLFYLPAKKNVDSILEDYTNYKKSRGNTDN

Parental  KEYAVNEVVAGIKEYFNVML-GT-QLLYKFERPQYAEILADHPDAPMSQVYGAPHLLRLFVRIGAMLAYT
          KEYAVNEVVAGIKEYF.VML.GT.QLLYKFER.QYAEILADHPDAPMSQVYGAPHL..LFVRIGAML.YT
Retrocopy KEYAVNEVVAGIKEYFSVML<GT<QLLYKFERLQYAEILADHPDAPMSQVYGAPHL*-LFVRIGAMLVYT

Parental  PLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVAPPEYHRKAV
          PLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEV.PPE.H.KAV
Retrocopy PLDEKSLALLLNYLHDFLKYLAKNSATLFSASDYEVVPPEHHQKAV

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	0.07 RPM	41.34 RPM
SRP051959_heart	0.21 RPM	63.99 RPM
SRP051959_kidney	0.24 RPM	72.19 RPM
SRP051959_liver	0.11 RPM	40.90 RPM
SRP051959_lung	0.24 RPM	58.89 RPM
SRP051959_lymph_node	0.27 RPM	43.58 RPM
SRP051959_skeletal_muscle	0.13 RPM	34.22 RPM
SRP051959_spleen	0.21 RPM	52.25 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2574 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2574 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2574 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,