RetrogeneDB ID: retro_ggor_1820

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 2b:123132412..123133255(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSGGOG00000006582
• Aliases: None
• Description: None

Sequence

>retro_ggor_1820
GTGCCTTATATCCCAGCAGAAAAGAATGCTGACCTTTGTAAGGAGATGGTGGATGGATTAAGAATAACCTTTGATTACAT
TCTCCCGTTGGTTTTACTCTAACCCTATGAACAAGCTCCGTATAAAAAGGTGACTGCATCTAAGGTTTTTCTTGCAATTA
AGGAAAGTGCCACAAATACTAATAGGAGCCAGGAGAAGCTCTCACCCAGCCCACGTTTGTTGAATCCATCCAGTCTGCAG
TCTACAGACAGTCAGTCGACCAGTGGTGAACGAGCCACCCCCAAAAGGCGCAAAGCCAAGACGCAAGCAGTGCAGTCTCT
GAGGCAGTCCTCGCCCCACACCGCCAACTGTGACAGGCTTTCTAAGAGCAGCACCTCACCTCAGCCCAAGCGCTGGCAGC
AGGACATGTCCACCAGCATGCCCAAGCTGTTTCTGCACCTGGAAAAGAAGACACCTATGCATAGCAGATCATCTTCACCT
ATTCCTCTGACTCCTGGCCAGGAAGGGAGTCCTGTGTTTGCTGGCTTTGAAGGGAGAAGAAGAACTAATGAAATAAATGA
GGTCCTCTCCTGGAAGCTCGTACCTGACAATTACCCACCAGGTGACCAGCCACCTCCACCCTCTTACATTTACGGGGCGC
AACATTTGCTGCGATTGTTTGTAAAACTTCCAGAAATTCTTGGAAAAATGTCCTTTACTGAGAAGAATCTGAAGGCTTTA
TTGAAGCACTCTTATCTCTTTGTGAGGTTTTTAGCAGAATACCACGATGACTTCTTCCCAGAGTCGGCTTATGTCACTGC
CTCTGAGGTGCGTTACAGCACCAAGAACCCCCAGGCAGTCTAT

Alignment

ORF - retro_ggor_1820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.69 %
• Parental protein coverage: 53.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSPS
          V.YIPAEKN.DLCKEMVDGLRITFDY.LPLVLL.PYEQA.YKKVT.SK.FL.IKESAT.TNRSQE.LSPS
Retrocopy VPYIPAEKNADLCKEMVDGLRITFDYILPLVLL*PYEQAPYKKVTASKVFLAIKESATNTNRSQEKLSPS

Parental  PPLLNPSTPQSTESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANCDRLSESSASPQPKRRQQDTSASM
          P.LLNPS..QST.SQ.T.GE.ATPKRRKA...A.QSLR.S..H.ANCDRLS.SS.SPQPKR.QQD.S.SM
Retrocopy PRLLNPSSLQSTDSQSTSGERATPKRRKAKTQAVQSLRQSSPHTANCDRLSKSSTSPQPKRWQQDMSTSM

Parental  PKLFLHLEKKETPVHSRSSSPIPLTPSKEGSAVFAGFEG-RRTNEINEVLSWKLVPDNYPPGDQPPPPSY
          PKLFLHLEKK.TP.HSRSSSPIPLTP..EGS.VFAGFEG.RRTNEINEVLSWKLVPDNYPPGDQPPPPSY
Retrocopy PKLFLHLEKK-TPMHSRSSSPIPLTPGQEGSPVFAGFEGRRRTNEINEVLSWKLVPDNYPPGDQPPPPSY

Parental  IYGAQHLLRLFVKLPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHDDFFPESAYVAACEAHYSTKNPRA
          IYGAQHLLRLFVKLPEILGKMSF.EKNLKALLKH..LF.RFLAEYHDDFFPESAYV.A.E..YSTKNP.A
Retrocopy IYGAQHLLRLFVKLPEILGKMSFTEKNLKALLKHSYLFVRFLAEYHDDFFPESAYVTASEVRYSTKNPQA

Parental  IY
          .Y
Retrocopy VY

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	0.05 RPM	24.36 RPM
SRP007412_cerebellum	0.08 RPM	13.47 RPM
SRP007412_heart	0.19 RPM	3.63 RPM
SRP007412_kidney	0.12 RPM	13.37 RPM
SRP007412_liver	0.18 RPM	14.16 RPM
SRP007412_testis	4.25 RPM	32.94 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_1820 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1820 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2401
Pan troglodytes	retro_ptro_1751
Pongo abelii	retro_pabe_2166

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820 , retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362, retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751, retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,