RetrogeneDB ID: retro_ggor_2378

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:122037477..122038610(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM14A
• Ensembl ID: ENSGGOG00000001762
• Aliases: None
• Description: None

Sequence

>retro_ggor_2378
TGTGAGCCACCAAAACCACAGTGTTCTTTGCCTGAAGACCCAGCTATCCTTCAGTCCTCACTGGGCTCATCAACTTCTTC
ATTCCGGTGTGTGGGGTTCTCATGGGCCTTTGGGCAGGATGCTCATATACAGTCGGTTCAGTCCAAGCTCCTTAGTTGGG
CAGGAGTTTGGTGCCGTTGCTGTTGCTGGAAGCTCTTTGACATCGTTTGGAACAGAAACATCAAACAGTGGTGTCTTTCC
CCAAAGTAGTGTGGTTGACTCTGCCTTAACACAGGATACAAGATCTCTAAAAACACAGTTATCTCAAGGTCACTCAAGCC
CTCAATTAGACCCTTTGAGAAAAAGCCCAACCACTGAACAAGCAGTGAAGACTGTCTCGGCCCATTTACCTGCTCCAGCA
CCTGTTGGGAGAAGGAGCCCTGTATCAACTATGCCTTTGCCATCTACTAGCCAAAAAGCAATAGAGATCAAGAGCACTGG
TGAGCTGAAGTACACAATGTTTCAAGACCAGAAAATGAGCAACTCAGAAATGATAGCAAGAGACAAGTAGCTCCAGGTAC
TCCTTCGGCTCCAAAGAGAGGGCGTGGGGTTCAGCCGGGTAGCAGGGGAAGATTTGGTATTCTGCGAGATGGGCCAATGA
AATTTGAGAAAGACTTTGACTTTGAAAGTGCAAATGCACAATTCAACAAGGGAGAGATCGACAGAGAGTTTCATAATAAA
CTTAAAAGAAGATAAACTGAGAAACAGGAGGAGCCTGTAAATGGTGAAGATAAAGGTGACCCAGGAGTTAATACCCCAAA
AGTAAAGGAAATGCTGATGAAGAAGATCCACTTGGACCTAACTGCTAGCAGGAAAAAACTAAATCCTTCTTTGATAATAT
TTCTTGTGATGACAATAGGGAACGGATATCAACCTGGGCTGAAGAAAGAAGATTAAATGCTGAAACATTTGGAATCCCAC
TTTGTCCAAATCGTGGCTGTGGGAGACGCAGAGGCAGAGGGATCTTCGGTTTCTGTGGTGGCAGAGGGCATGGTGATAGC
AGATGTGGTACTTTAACCATCCCTGGAAGATTTCGCAGTGGATTCAGAGGAGGTCCTGGGGGCAGGGAGTTTTCGGATTT
CTAATGTAGGAAA

Alignment

ORF - retro_ggor_2378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.63 %
• Parental protein coverage: 83.15 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CEPPKPQCSLPQDPAIVQSSLGSSTSSFQSMG-SYGPFGRMPTYSQFSPSSLVGQQFGAVGVAGSSLTSF
          CEPPKPQCSLP.DPAI.QSSLGSSTSSF...G.S.GP.GRM..YS.FSPSSLVGQ.FGAV.VAGSSLTSF
Retrocopy CEPPKPQCSLPEDPAILQSSLGSSTSSFRCVG>SHGPLGRMLIYSRFSPSSLVGQEFGAVAVAGSSLTSF

Parental  GTETSNSGTLPQSSAVGSAFTQDTRSLKTQLSQGRSSPQLDPLRKSPTMEQAVQTASAHLPAPAAVGRRS
          GTETSNSG..PQSS.V.SA.TQDTRSLKTQLSQG.SSPQLDPLRKSPT.EQAV.T.SAHLPAPA.VGRRS
Retrocopy GTETSNSGVFPQSSVVDSALTQDTRSLKTQLSQGHSSPQLDPLRKSPTTEQAVKTVSAHLPAPAPVGRRS

Parental  PVSTRPLPSASQKAGE-NQEHRRAEVHKVSRPENEQLRNDNKRQVAPGAPSAPRRGRGGHRGGRGRFGIR
          PVST.PLPS.SQKA.E..QEH..AEVH.VSRPENEQLRND.KRQVAPG.PSAP.RGRG...G.RGRFGI.
Retrocopy PVSTMPLPSTSQKAIE<DQEHW*AEVHNVSRPENEQLRNDSKRQVAPGTPSAPKRGRGVQPGSRGRFGIL

Parental  RDGPMKFEKDFDFESANAQFNKEEIDREFHNKLKLKEDKLEKQEKPVNGEDKGDSGVDT-QNSEGNADEE
          RDGPMKFEKDFDFESANAQFNK.EIDREFHNKLK......EKQE.PVNGEDKGD.GV.T...S.GNADEE
Retrocopy RDGPMKFEKDFDFESANAQFNKGEIDREFHNKLKRR--*TEKQEEPVNGEDKGDPGVNT<PKSKGNADEE

Parental  DPLGPNCYYDKTKSFFDNISCDDNRERRPTWAEERRLNAETFGIPLRPNRGRGGYRGRGGLGFRGGRGRG
          DPLGPNC...KTKSFFDNISCDDNRER..TWAEERRLNAETFGIPL.PNRG.G..RGRG..GF.GGRG.G
Retrocopy DPLGPNC*QEKTKSFFDNISCDDNRERISTWAEERRLNAETFGIPLCPNRGCGRRRGRGIFGFCGGRGHG

Parental  GGRGGTFTAPRGFRGGFRGGRGGREFADFEYRK
          ..R.GT.T.P..FR.GFRGG.GGREF.DF..RK
Retrocopy DSRCGTLTIPGRFRSGFRGGPGGREFSDF*CRK

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	0.00 RPM	53.13 RPM
SRP007412_cerebellum	0.00 RPM	75.84 RPM
SRP007412_heart	0.03 RPM	29.99 RPM
SRP007412_kidney	0.00 RPM	103.45 RPM
SRP007412_liver	0.00 RPM	57.87 RPM
SRP007412_testis	0.41 RPM	159.54 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_2378 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2378 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2389
Pongo abelii	retro_pabe_2906
Macaca mulatta	retro_mmul_1860

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006555	1 retrocopy	retro_chof_1375,
Gorilla gorilla	ENSGGOG00000001762	1 retrocopy	retro_ggor_2378 ,
Microcebus murinus	ENSMICG00000011598	1 retrocopy	retro_mmur_1605,
Myotis lucifugus	ENSMLUG00000003368	1 retrocopy	retro_mluc_1793,
Macaca mulatta	ENSMMUG00000021614	2 retrocopies	retro_mmul_1386, retro_mmul_1860,
Nomascus leucogenys	ENSNLEG00000011713	4 retrocopies	retro_nleu_1299, retro_nleu_2544, retro_nleu_2580, retro_nleu_485,
Oryctolagus cuniculus	ENSOCUG00000011872	2 retrocopies	retro_ocun_193, retro_ocun_860,
Otolemur garnettii	ENSOGAG00000002492	2 retrocopies	retro_ogar_2586, retro_ogar_67,
Pongo abelii	ENSPPYG00000009832	2 retrocopies	retro_pabe_1693, retro_pabe_2906,
Pan troglodytes	ENSPTRG00000010813	3 retrocopies	retro_ptro_1343, retro_ptro_2389, retro_ptro_863,
Rattus norvegicus	ENSRNOG00000021133	1 retrocopy	retro_rnor_2397,
Ictidomys tridecemlineatus	ENSSTOG00000002785	1 retrocopy	retro_itri_170,