RetrogeneDB ID: retro_cjac_1174

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 13:105291129..105292776(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000002988
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSCJAG00000004530
• Aliases: None
• Description: None

Sequence

>retro_cjac_1174
CATCCAAGTTTATATTTTGATGGTGGAGAAATCCAAGCAATGAGACAAAAGTCTCGCACAAGCCATTTGCATCTTTTTAG
AGCTATCAGAAGTGCAGTGACAGTTATGCTGTCCAACCCAACATACTACCTACCTCCACCAAAGCATGCTGATTTTGCTG
CCAAGTGGAACGAAATTTATGGTAACAATCTGCCTCCTTTAGCATTGTACTGTTTGTTATGCCCAGAAGACAAAGTTGCC
TTTGAGTTTGTCTTGGAATATATGGACAGGATGGTTGGCTACAAAGACTGGCTAGTAGAGAATGCACCAGGAGATGAGGT
TCCAATTGGCCATTCCTTAACAGGTTTTGCCACTGCCTTTGACTTTTTATATAACTTACTAGATAATCATCGAAGACAAA
AATACCTGGAAAAAATATGGGTTATTACTGAGGAAATGTATGAGTATTCCAAGGTCCGCTCATGGGGCAAACAGCTTCTC
CATAACCACCAAGCCACTAATATGATAGCGTTACTCACAGGGGCCTTGGTGACTGGAGTAGATAAAGGATCTAAAGCAAA
TATATGGAAACAGGTTGTAGTGGATGTAATGGAAAAGACGATGTTTCTACTGAATCATATTGTTGATGGTTCTTTGGATG
AAGGTGTGGCCTATGGAAGCTACACAGCTAAATCCATCACACAGTATGTTTTTCTGGCCCAGCGCCATTTTAATATCAAT
AACTTGGATAATAACTGGTTAAAGATGCACTTTTGGTTCTATTATGCCACCCTTTTACCTGGCTTCCAAAGAACTGTGGG
TATAGCAGATTCCAATTATAATTGGTTTTATGGGCCAGAGAGCCAGCTAGTTTTCTTGGATAAGTTCATCTTAAAGAATG
GAGCCGGAAATTGGTTAGCTCAGCAAATTAGAAAGCACCGACCTAAAGATGGACCGATGGTTCCTTCAACTGCCCAGAGG
TGGAGTACTCTTCACACTGAATACATCTGGTATGATCCCCAGCTCATACCACAGCCACCTGCTGAATATGGTACTGCAAA
AATACACACATTCCCTAATTGGGGTGTGGTTACTTATGGGGCTGGGTTGCCAAACACACAAACTAATACCTTTGTGTCTT
TTAAATCTGGGAAGCTGGGGGGACGGGCTGTGTATGACATAGTTCATTTTCAGCCATATTCATGGATTGATGGGTGGAGA
AGCTTTAACCCAGGACATGAGCATCCAGATCAGAACTCATTTACTTTTGCCCCCAATGGACAAGTATTTGTTTCTGAAGC
TCTCTATGGACCCAAGTTGAGCCACCTTAACAATGTATTGGTGTTCGCTCCATCACCCTCAAGCCAGTGTAATAAGCCCT
GGGAAGGTCAACTGGGAGAATGTGCACAGTGGCTTAAGTGGACTGGTGAGGAGGTTGGTGATGCAGCTGGGGAAATCATC
ACTGCCTCTCAACATGGGGAAATGATATTTGTGAGTGGGGAAGCAGTGTCTGCTTATTCTTCAGCAATGAGACTGAAAAG
TGTGTATCGTGCTTTGCTTCTCTTAAATTCTCAAACTCTGCTAGTTGTTGATCATATTGAGAGGCAAGAAGATTCCCCAA
TAAATTCTGTCAGTGCCTTCTTTCATAATTTGGATATTGATTTTAAA

Alignment

ORF - retro_cjac_1174 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.61 %
• Parental protein coverage: 57.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HPMLYFSRAEVAELQLRAASSHEHIAARLTEAVHTMLSSPLEYLPPWDPKDYSARWNEIYGNNLGALAMF
          HP.LYF...E..........SH.H.......AV..MLS.P..YLPP....D..A.WNEIYGNNL..LA..
Retrocopy HPSLYFDGGEIQAMRQKSRTSHLHLFRAIRSAVTVMLSNPTYYLPPPKHADFAAKWNEIYGNNLPPLALY

Parental  CVLYPENIEARDMAKDYMERMAAQPSWLVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIA
          C.L.PE...A......YM.RM.....WLV..AP.DEVP..HSL.GFATA.DFLYN.L......K.LE.I.
Retrocopy CLLCPEDKVAFEFVLEYMDRMVGYKDWLVENAPGDEVPIGHSLTGFATAFDFLYNLLDNHRRQKYLEKIW

Parental  NASGYMYETSYRRGWGFQYLHNHQPTNCMALLTGSLVL-MNQGYLQEAYLWTKQVLTIMEKSLVLLREVM
          .....MYE.S..R.WG.Q.LHNHQ.TN..ALLTG.LV.....G....A..W...V...MEK...LL....
Retrocopy VITEEMYEYSKVRSWGKQLLHNHQATNMIALLTGALVTGVDKG--SKANIWKQVVVDVMEKTMFLLNHIV

Parental  DGSLYEGVAYGTYTTRSLFQYMFLVQRHFDINHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYG
          DGSL.EGVAYG.YT..S..QY.FL.QRHF.IN.....WLK.HF.F.Y.T.LPGFQRTV.IADSNYNWFYG
Retrocopy DGSLDEGVAYGSYTAKSITQYVFLAQRHFNINNLDNNWLKMHFWFYYATLLPGFQRTVGIADSNYNWFYG

Parental  PESQLVFLDKFVMRNGSGNWLADQIRRNRVVEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTL
          PESQLVFLDKF...NG.GNWLA.QIR..R...GP..PS..QRW.TLHTE..WYD..L...PP...GT...
Retrocopy PESQLVFLDKFILKNGAGNWLAQQIRKHRPKDGPMVPSTAQRWSTLHTEYIWYDPQLIPQPPAEYGTAKI

Parental  HYFEDWGVVTYGSALPAEINRSFLSFKSGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFA
          H.F..WGVVTYG..LP......F.SFKSGKLGGRA.YDIVH...Y..WI.GWR.FN.GHEHPDQNSFTFA
Retrocopy HTFPNWGVVTYGAGLPNTQTNTFVSFKSGKLGGRAVYDIVHFQPY-SWIDGWRSFNPGHEHPDQNSFTFA

Parental  PNGVPFITEALYGPKYTFFNNVLMFSPAVSKSCFSPWEGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEK
          PNG..F..EALYGPK....NNVL.F.P..S..C..PWEGQ..E.....W.K..........G....A...
Retrocopy PNGQVFVSEALYGPKLSHLNNVLVFAPSPSSQCNKPWEGQLGE--CAQWLKWTGEEVGDAAGEIITASQH

Parental  NGVVFIRGEGVGAYNPHLNLKNVQRNLILLHPQLLLLVDQIHLGEESPLEIAASFFHNVDVPFE
          ....F..GE.V.AY.....LK.V.R.L.LL..Q.LL.VD.I...E.SP......FFHN.D..F.
Retrocopy GEMIFVSGEAVSAYSSAMRLKSVYRALLLLNSQTLLVVDHIERQEDSPINSVSAFFHNLDIDFK

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	4.04 RPM	5.06 RPM
SRP051959_heart	11.49 RPM	9.82 RPM
SRP051959_kidney	3.42 RPM	4.95 RPM
SRP051959_liver	3.88 RPM	4.46 RPM
SRP051959_lung	3.61 RPM	8.39 RPM
SRP051959_lymph_node	1.42 RPM	5.34 RPM
SRP051959_skeletal_muscle	3.65 RPM	4.56 RPM
SRP051959_spleen	3.80 RPM	13.72 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1174 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1174 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1174 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_1419

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174 ,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,