RetrogeneDB ID: retro_cjac_2401

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 4:3110470..3111075(-)
• Located in intron of: ENSCJAG00000010693

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCJAG00000006953
• Aliases: None
• Description: None

Sequence

>retro_cjac_2401
ATGATGAAGTATTCCTAGGCCAGAATAGCCTCCTTTCTGAATCCAAATGCTCACTACCTTGAGTACATTGGTACTCAAAT
CCCTATAGCAAACATATTCTGACCAAAAACAAAGAATATGAGGAGCTGACCCCTGCCCAGAAGCTCCTGTCCCAGTGACT
CCTGACCAAGACCAAAGGGATGTCCTGCTGGGCTGAGTGGCTATTTCTTGCTAGTCATGCTCACCCAGCGTCCATCCTGG
CGGACTCTACTGCTCACCCACGGAATCAGAGGGAACCACCTTTACCTGCAGCGGCAACCACGCCCAGCTGACGGTGGTCC
AGGGAAGACGCGTTTACTTTGTGAAGTCTGACGACAGTGCTAGTCCGAGATCCCCAGGGAAGCTGAGTCTTCCCTGGCTT
ACCTAGTGTCTACGGAGCTGTCCAGGAACTCGGCCATGCTCTTTTCAAAGGCAACATGACCGAAACCGTGAAACGTTTTG
AGTACATCTTGGCCAAGCTGCCAGACAATGCACCTTCCAAAATACCTGCTGAGACAGCCCAAAAAGTCAAGGGGAAGTCA
AAGAAGACAGCACTGACCGCTGCAGAGAAGGCCAAGGAGCTGGCG

Alignment

ORF - retro_cjac_2401 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.02 %
• Parental protein coverage: 93.15 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MVKY-FLGQ-SLLRSSWDQVFAAFWQRYPNPYSKHVLTEDIVHREVTPDQKLLSRRLLTKTNRMPRWAER
          M.KY.FLGQ.SLL..S........W..Y.NPYSKH.LT......E.TP.QKLLS..LLTKT..M..WAE.
Retrocopy MMKY<FLGQNSLLSESKCSLP*VHW--YSNPYSKHILTKNKEYEELTPAQKLLSQ*LLTKTKGMSCWAEW

Parental  LFPANVAHSVYILEDSIVDPQNQTM-TTFTWNINHARLMVVEERCVYCVNSDNSGW-TEIRREAWVSSS-
          LF.A..AH...IL.DS...P.NQ...TTFT...NHA.L.VV..R.VY.V.SD.S....EI.REA..S...
Retrocopy LFLASHAHPASILADSTAHPRNQRE<TTFTCSGNHAQLTVVQGRRVYFVKSDDSAS<SEIPREAESSLA<

Parental  LFGVSRAVQEFGLARFKSNVTKTMKGFEYILAKLQGEAPSKTLVETAKEAKEKAKETALAATEKAKDLA
          L..V..AVQE.G.A.FK.N.T.T.K.FEYILAKL...APSK...ETA...K.K.K.TAL.A.EKAK.LA
Retrocopy LPSVYGAVQELGHALFKGNMTETVKRFEYILAKLPDNAPSKIPAETAQKVKGKSKKTALTAAEKAKELA

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	19.17 RPM
SRP051959_heart	0.02 RPM	6.37 RPM
SRP051959_kidney	0.00 RPM	18.99 RPM
SRP051959_liver	0.00 RPM	19.49 RPM
SRP051959_lung	0.05 RPM	10.28 RPM
SRP051959_lymph_node	0.00 RPM	11.94 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.85 RPM
SRP051959_spleen	0.00 RPM	12.18 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2401 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2401 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2401 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3565
Gorilla gorilla	retro_ggor_2404
Macaca mulatta	retro_mmul_1822

---

Parental genes homology:

Parental genes homology involve 23 parental genes, and 81 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005009	2 retrocopies	retro_btau_1727, retro_btau_962,
Canis familiaris	ENSCAFG00000016443	2 retrocopies	retro_cfam_2055, retro_cfam_349,
Choloepus hoffmanni	ENSCHOG00000002251	1 retrocopy	retro_chof_1025,
Callithrix jacchus	ENSCJAG00000006953	5 retrocopies	retro_cjac_1131, retro_cjac_1689, retro_cjac_2401 , retro_cjac_3359, retro_cjac_835,
Cavia porcellus	ENSCPOG00000025788	1 retrocopy	retro_cpor_231,
Dasypus novemcinctus	ENSDNOG00000017550	1 retrocopy	retro_dnov_637,
Equus caballus	ENSECAG00000023460	1 retrocopy	retro_ecab_467,
Homo sapiens	ENSG00000169230	7 retrocopies	retro_hsap_1550, retro_hsap_2269, retro_hsap_249, retro_hsap_302, retro_hsap_3518, retro_hsap_3565, retro_hsap_579,
Gorilla gorilla	ENSGGOG00000011762	3 retrocopies	retro_ggor_2404, retro_ggor_302, retro_ggor_9,
Loxodonta africana	ENSLAFG00000005459	1 retrocopy	retro_lafr_242,
Macropus eugenii	ENSMEUG00000001738	12 retrocopies	retro_meug_1194, retro_meug_1541, retro_meug_1618, retro_meug_1725, retro_meug_1726, retro_meug_2054, retro_meug_274, retro_meug_666, retro_meug_681, retro_meug_854, retro_meug_895, retro_meug_918,
Myotis lucifugus	ENSMLUG00000007008	2 retrocopies	retro_mluc_239, retro_mluc_64,
Macaca mulatta	ENSMMUG00000009046	2 retrocopies	retro_mmul_1822, retro_mmul_2457,
Monodelphis domestica	ENSMODG00000004804	3 retrocopies	retro_mdom_1529, retro_mdom_221, retro_mdom_596,
Mustela putorius furo	ENSMPUG00000012226	1 retrocopy	retro_mputfur_579,
Mus musculus	ENSMUSG00000021486	7 retrocopies	retro_mmus_1316, retro_mmus_2079, retro_mmus_2236, retro_mmus_2394, retro_mmus_2672, retro_mmus_449, retro_mmus_866,
Nomascus leucogenys	ENSNLEG00000012714	5 retrocopies	retro_nleu_1382, retro_nleu_2395, retro_nleu_2400, retro_nleu_803, retro_nleu_857,
Otolemur garnettii	ENSOGAG00000011455	4 retrocopies	retro_ogar_1352, retro_ogar_2025, retro_ogar_3006, retro_ogar_665,
Pongo abelii	ENSPPYG00000016086	7 retrocopies	retro_pabe_1283, retro_pabe_1696, retro_pabe_1699, retro_pabe_2907, retro_pabe_377, retro_pabe_409, retro_pabe_608,
Rattus norvegicus	ENSRNOG00000016410	8 retrocopies	retro_rnor_1138, retro_rnor_1166, retro_rnor_1243, retro_rnor_1906, retro_rnor_2178, retro_rnor_2305, retro_rnor_637, retro_rnor_995,
Sus scrofa	ENSSSCG00000014042	4 retrocopies	retro_sscr_372, retro_sscr_794, retro_sscr_795, retro_sscr_811,
Tupaia belangeri	ENSTBEG00000006445	1 retrocopy	retro_tbel_3855,
Tursiops truncatus	ENSTTRG00000009571	1 retrocopy	retro_ttru_1886,