RetrogeneDB ID: retro_ggor_1419

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 18:65803777..65805133(-)
• Located in intron of: ENSGGOG00000026085

Retrocopy information

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

Parental gene information

• Parental gene symbol: DSE
• Ensembl ID: ENSGGOG00000026746
• Aliases: None
• Description: None

Sequence

>retro_ggor_1419
CTAGTAGAGAATGCACCAGGAGATGAGGTTCCAATTGGCCATTCCTTAACAGGTTTTGCCACTGCCTTTGACTTTTTATA
TAACTTATTAGATAATCATCGAAGACAAAAATACCTGGAAAAAATATGGGTTATTACTGAGGAAATGTATGAGTATTCCA
AGGTCCGCTCATGGGGCAAACAGCTTCTCCATAACCACCAAGCCACTAACATGATAGCATTACTCACAGGGGCCTTGGTG
ACTGGAGTAGATAAAGGATCTAAAGCAAATATATGGAAACAGGCTGTAGTGGATGTCATGGAAAAGACAATGTTTCTATT
GAATCATATTGTTGATGGTTCTCTGGATGAAGGTGTGGCCTATGGAAGCTACACAGCTAAATCCGTCACACAGTATGTTT
TTCTGGCCCAGCGCCATTTTAATATCAACAACTTGGATAATAACTGGTTAAAGATGCACTTTTGGTTCTATTATGCCACC
CTTTTACCTGGCTTCCAAAGAACTGTGGGTATAGCAGATTCCAATTATAATTGGTTTTATGGTCCAGAAAGCCAGCTAGT
TTTCTTGGATAAGTTCATCTTAAAGAATGGAGCTGGAAATTGGTTAGCTCAGCAAATTAGAAAGCACCGACCTAAAGATG
GACCGATGGTTCCTTCAACTGCCCAAAGGTGGAGTACTCTTCACACTGAATACATCTGGTATGATCCCCAGCTCACACCA
CAGCCACCTGCTGATTATGGTACTGCAAAAATACACACATTCCCTAACTGGGGTGTGGTTACTTATGGGGCTGGGTTGCC
AAACACACAGACCAACACCTTTGTGTCTTTTAAATCTGGGAAGCTGGGGGGACGAGCTGTGTATGACATAGTTCATTTTC
AGCCATATTCCTGGATTGATGGGTGGAGAAGTTTTAACCCAGGACATGAGCATCCAGATCAGAACTCATTTACTTTTGCC
CCCAATGGACAAGTATTTGTTTCTGAAGCTCTCTATGGACCCAAGTTGAGCCACCTTAACAATGTATTGGTGTTTGCTCC
ATCACCCTCAAGCCAGTGTAATAAGCCCTGGGAAGGTCAACTGGGAGAATGTGCTCAGTGGCTTAAGTGGACTGGCGAGG
AGGTTGGTGATGCAGCTGGGGAAATAATCACTGCCTCTCAACATGGGGAAATGGTATTTGTGAGTGGGGAAGCCGTGTCT
GCTTATTCTTCAGCGATGAGACTGAAAAGTGTATATCGTGCTTTGCTTCTCTTAAATTCCCAAACTCTGCTAGTTGTTGA
TCATATTGAGAGGCAAGAAGATTCCCCAATAAATTCTGTCAGTGCCTTCTTTCATAATTTGGATATTGATTTTAAA

Alignment

ORF - retro_ggor_1419 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.46 %
• Parental protein coverage: 55.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVKDAPWDEVPLAHSLVGFATAYDFLYNYLSKTQQEKFLEVIANASGYMYETSYRRGWGFQYLHNHQPTN
          LV..AP.DEVP..HSL.GFATA.DFLYN.L......K.LE.I......MYE.S..R.WG.Q.LHNHQ.TN
Retrocopy LVENAPGDEVPIGHSLTGFATAFDFLYNLLDNHRRQKYLEKIWVITEEMYEYSKVRSWGKQLLHNHQATN

Parental  CMALLTGSLVL-MNQGYLQEAYLWTKQVLTIMEKSLVLLREVTDGSLYEGVAYGSYTTRSLFQYMFLVQR
          ..ALLTG.LV.....G....A..W...V...MEK...LL....DGSL.EGVAYGSYT..S..QY.FL.QR
Retrocopy MIALLTGALVTGVDKG--SKANIWKQAVVDVMEKTMFLLNHIVDGSLDEGVAYGSYTAKSVTQYVFLAQR

Parental  HFNINHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSGNWLADQIRR
          HFNIN.....WLK.HF.F.Y.T.LPGFQRTV.IADSNYNWFYGPESQLVFLDKF...NG.GNWLA.QIR.
Retrocopy HFNINNLDNNWLKMHFWFYYATLLPGFQRTVGIADSNYNWFYGPESQLVFLDKFILKNGAGNWLAQQIRK

Parental  NRVVEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDWGVVTYGSALPAEINRSFLSFK
          .R...GP..PS..QRW.TLHTE..WYD..L...PP.D.GT...H.F..WGVVTYG..LP......F.SFK
Retrocopy HRPKDGPMVPSTAQRWSTLHTEYIWYDPQLTPQPPADYGTAKIHTFPNWGVVTYGAGLPNTQTNTFVSFK

Parental  SGKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSP
          SGKLGGRA.YDIVH...Y..WI.GWR.FN.GHEHPDQNSFTFAPNG..F..EALYGPK....NNVL.F.P
Retrocopy SGKLGGRAVYDIVHFQPY-SWIDGWRSFNPGHEHPDQNSFTFAPNGQVFVSEALYGPKLSHLNNVLVFAP

Parental  AVSKSCFSPWVGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNL
          ..S..C..PW.GQ..E.....W.K..........G....A......VF..GE.V.AY.....LK.V.R.L
Retrocopy SPSSQCNKPWEGQLGE--CAQWLKWTGEEVGDAAGEIITASQHGEMVFVSGEAVSAYSSAMRLKSVYRAL

Parental  ILLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFE
          .LL..Q.LL.VD.I...E.SP......FFHN.D..F.
Retrocopy LLLNSQTLLVVDHIERQEDSPINSVSAFFHNLDIDFK

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
SRP007412_brain_prefrontal_cortex	3.21 RPM	3.50 RPM
SRP007412_cerebellum	3.39 RPM	4.45 RPM
SRP007412_heart	0.56 RPM	2.66 RPM
SRP007412_kidney	6.30 RPM	14.27 RPM
SRP007412_liver	2.66 RPM	16.12 RPM
SRP007412_testis	4.35 RPM	9.32 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_1419 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1419 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Callithrix jacchus	retro_cjac_1174

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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,