RetrogeneDB ID: retro_cjac_2003

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 20:6956274..6957046(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MTCH2
• Ensembl ID: ENSCJAG00000020213
• Aliases: None
• Description: mitochondrial carrier 2 [Source:HGNC Symbol;Acc:17587]

Sequence

>retro_cjac_2003
ATGGAAGATGTAGCCAGTCAGGTGCTTCTGGGCTCTGGTCTCACCATGCAGTCTCAGCAGCTTATGTATGTGAAAGTGCT
CATCCAAGTGGGAGGTAAGCGTATTTTTCCAACAACAGGACAACATATTTTTGGGTGGCATGTCAGCTTCCTGGTCTCTT
TAGTTGTGCTTAGCACATTATAAGCATCAGTGAGTGGCCTTAGCACATTGTGAACATCAACTCCAAGGCTGTGTTCAAGA
GTCCCTGAAAATATGATTCATGGTAAAGTTTTACGGCATTACCAGGAATGTGACAAGATTGAGGAGTTAGGGCTTGGTGA
TGTACAGAAAGAAGTCTCATCTTCTTTTGATCAAGTTATCAAGAAGACAGTTTGAGAGATGATCACTCATTTTGCTGCTG
TCCTCATCACAAATCCCTTCCATATGATCACTGAGGTACAATTCATTGTCAGAGAATCCAAATACTGCAGACTTTGTGAT
TCCATAGTAACCATCTCTCAGGGAGAAGGCATCCTATGATTTTTCATGAATCTTGTTCCTCACTTCCAAGGTGACATCAT
TTCTTTGTGACTCTGTAACTTGCTGGCCTATCTCATCATATCTGTTTACTAAACAGTGGGGTTTCCACCACGAATGAAAT
AAAGAATTATTCCCAAGTCGTTACAGAAACTTTTGCCAGTATGTTGATCTAATCTGTTGTGTTTGTCTCTAATCTTATGT
ATGTTGACAGCTGCAGCTTGCTGGTGGATCCTCTCCTTATTGGCCAGTGTAT

Alignment

ORF - retro_cjac_2003 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.12 %
• Parental protein coverage: 86.47 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADAASQVLLGSGLTILSQPLMYVKVLIQVGYEPLPPTIGRNIFGRQVCQLPGLFCYAQHIASIDGRRGL
          M.D.ASQVLLGSGLT..SQ.LMYVKVLIQVG.....PT.G..IFG..V..L..L.......AS..G...L
Retrocopy MEDVASQVLLGSGLTMQSQQLMYVKVLIQVGGKRIFPTTGQHIFGWHVSFLVSLVVLSTL*ASVSGLSTL

Parental  FTGLTPRLCSGVLGTVVHGKVLQHYQESDKGEELGPGNVQKEVSSSFDRVIKETTREMIARSAATLITHP
          .T..TPRLCS.V.....HGKVL.HYQE.DK.EELG.G.VQKEVSSSFD.VIK.T..EMI...AA.LIT.P
Retrocopy *TS-TPRLCSRVPENMIHGKVLRHYQECDKIEELGLGDVQKEVSSSFDQVIKKTV*EMITHFAAVLITNP

Parental  FHVITLRSMVQFIGRESKYCGLCDSIVTIYREEGILGFFAGLVPRLLGDILSLWLCNSLAYLV-NTYALD
          FH.IT....VQFI.RESKYC.LCDSIVTI...EGIL.FF..LVP...GDI.SL.LCN.LAYL......L.
Retrocopy FHMIT---EVQFIVRESKYCRLCDSIVTISQGEGIL*FFMNLVPHFQGDIISL*LCNLLAYLI<HICLLN

Parental  SGVSTMNEMKSYSQAVTGFFASMLTYPFVLVSNLMAVNNCG-LAGGCPPYSPIY
          SGVST.NE.K.YSQ.VT..FASML....V.VSNLM.V..C..LAGG..PY.P.Y
Retrocopy SGVSTTNEIKNYSQVVTETFASMLI*SVVFVSNLMYVDSCS<LAGGSSPYWPVY

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	30.84 RPM
SRP051959_heart	0.00 RPM	23.77 RPM
SRP051959_kidney	0.00 RPM	42.07 RPM
SRP051959_liver	0.00 RPM	29.52 RPM
SRP051959_lung	0.00 RPM	16.12 RPM
SRP051959_lymph_node	0.00 RPM	22.62 RPM
SRP051959_skeletal_muscle	0.00 RPM	35.73 RPM
SRP051959_spleen	0.00 RPM	20.48 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_2003 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_2003 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_2003 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018742	1 retrocopy	retro_btau_1321,
Choloepus hoffmanni	ENSCHOG00000008473	1 retrocopy	retro_chof_2162,
Callithrix jacchus	ENSCJAG00000005273	2 retrocopies	retro_cjac_2480, retro_cjac_4182,
Callithrix jacchus	ENSCJAG00000020213	3 retrocopies	retro_cjac_1551, retro_cjac_2003 , retro_cjac_3812,
Dasypus novemcinctus	ENSDNOG00000001221	1 retrocopy	retro_dnov_1867,
Homo sapiens	ENSG00000109919	2 retrocopies	retro_hsap_1041, retro_hsap_1690,
Gorilla gorilla	ENSGGOG00000008281	3 retrocopies	retro_ggor_1267, retro_ggor_3083, retro_ggor_822,
Mustela putorius furo	ENSMPUG00000003852	1 retrocopy	retro_mputfur_312,
Mus musculus	ENSMUSG00000027282	1 retrocopy	retro_mmus_2657,
Nomascus leucogenys	ENSNLEG00000014704	2 retrocopies	retro_nleu_1335, retro_nleu_913,
Oryctolagus cuniculus	ENSOCUG00000006368	2 retrocopies	retro_ocun_1197, retro_ocun_983,
Otolemur garnettii	ENSOGAG00000011607	1 retrocopy	retro_ogar_2578,
Pongo abelii	ENSPPYG00000003296	3 retrocopies	retro_pabe_1392, retro_pabe_1894, retro_pabe_872,
Pan troglodytes	ENSPTRG00000003573	2 retrocopies	retro_ptro_1144, retro_ptro_710,
Pteropus vampyrus	ENSPVAG00000007348	1 retrocopy	retro_pvam_954,
Sorex araneus	ENSSARG00000001399	1 retrocopy	retro_sara_705,
Sus scrofa	ENSSSCG00000013232	3 retrocopies	retro_sscr_262, retro_sscr_279, retro_sscr_602,
Tursiops truncatus	ENSTTRG00000014169	2 retrocopies	retro_ttru_1476, retro_ttru_353,