RetrogeneDB ID: retro_ggor_2403

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 6:25838552..25839779(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASS1
• Ensembl ID: ENSGGOG00000010228
• Aliases: None
• Description: None

Sequence

>retro_ggor_2403
ATGTCCAGCAAAGGCTCCATGAGAGTTCTGGCCTATGGTGGCAGCCTGGACACCTCCTGCATCCTCGTGTGGGTGAAGGA
ACAAGGCTATGATGTCATTGCCTACCTGGCCAACACTGGCCAGAAGGAAGACTTCGAGGAAGCCAGGAAGAAGGCACTGA
AACTTGGGGCCAAAAAGGTGTGCATTGAGGATGTCATCAGGGAGTTTGTGGAAGAGTTCATCTGGCCGGCCATCCAGTCC
AGCACACTGTATGAGGACCGCTACCTCCTGGGCACCTTTCTCGCCAGGCCCTGCATTGCCAGCAAACAAGTGGAAATCGC
CCAGCAGGAGGGGGTGTCCCGCGGCGCCACGGGTAAGGGGAATGATCAGGTCCGGTTTGAGCTCACCTGGTACTCGCTGG
TCCCCCAGATAAAGGGCACTGCTCCCTGGAGGATGCCCAAGTTCTACAACCGGTTCAAGGGCCGTAATGACCTGATGGAA
TACGCAAAGCAGCACGGGATTCCTATCCCGGTCACTCCCAAGAACCCGTGGAACATGGACGAGAACCTCATGCACATCAG
CTACGAGGCTGGAATCCTGGAGAACCCCAAGAACCAAGTGCCTCCAGGTCTCTACACGAAGACCTAGGAACAGGTCAAAG
CCCCCAACACCCCTGACATCCTCGAGATCGAGTTAAAAAAAGGGGTCCCCGTGAAGGTGACCAACGTCAAGGATGGCTCC
ACCCACCCGACCTCCTTCACGTACCTGAACGAAGTCGCGGACAAACACGGTGTGGGCTGTACTGACATCGTGGAGAACCG
CTTCACTGGAATGAAGTCCCGGGGTATCTATGAGACCCCAGCAGGCACCATCCTGTACCACACTCATTTAGACATCGAGG
CCTTCACCATGGACTGGGAGGTGTGCAAAATCAAACAAGGCCTGGGCTTGAAATTTGCTGAGCTGGTGTACACCGCTTTC
TGGCATAGCCCTGAGTGTGAATTTGTCCGCCACTGCATCGCCAAGTCCTAGGTGCAAGTGGGAGGGAAAGCGCAGGTGTC
CGTCCTCAAGGGCCAGGTGTACATCCTTGGCTGGGAGTGCCCACTCTCTCCCTACAACGAGGAGCCGGTGAGCATGAACG
TGCAGGGTGATTATGAGCCAATTGATGCCACCGGGTTCATCAACATCAATTCCCTCAGGCTGAAGGAATAGGAATATCAT
CGTCTCCAGAGCAAGGTCACTGCCAAA

Alignment

ORF - retro_ggor_2403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.51 %
• Parental protein coverage: 99.76 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSKGSV-VLAYSGGLDTSCILVWLKEQGYDVIAYLANIGQKEDFEEARKKALKLGAKKVFIEDVSREFV
          MSSKGS..VLAY.G.LDTSCILVW.KEQGYDVIAYLAN.GQKEDFEEARKKALKLGAKKV.IEDV.REFV
Retrocopy MSSKGSMRVLAYGGSLDTSCILVWVKEQGYDVIAYLANTGQKEDFEEARKKALKLGAKKVCIEDVIREFV

Parental  EEFIWPAIQSSALYEDRYLLGTSLARPCIARKQVEIAQREGAKYVSHGATGKGNDQVRFELSCYSLAPHI
          EEFIWPAIQSS.LYEDRYLLGT.LARPCIA.KQVEIAQ.EG...VS.GATGKGNDQVRFEL..YSL.P.I
Retrocopy EEFIWPAIQSSTLYEDRYLLGTFLARPCIASKQVEIAQQEG---VSRGATGKGNDQVRFELTWYSLVPQI

Parental  KVIAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTK
          K..APWRMP.FYNRFKGRNDLMEYAKQHGIPIPVTPKNPW.MDENLMHISYEAGILENPKNQ.PPGLYTK
Retrocopy KGTAPWRMPKFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWNMDENLMHISYEAGILENPKNQVPPGLYTK

Parental  TQDPAKAPNTPDILEIEFKKGVPVKVTNVKDGTTHQTSLELFMYLNEVAGKHGVGRIDIVENRFIGMKSR
          T....KAPNTPDILEIE.KKGVPVKVTNVKDG.TH.TS...F.YLNEVA.KHGVG..DIVENRF.GMKSR
Retrocopy T*EQVKAPNTPDILEIELKKGVPVKVTNVKDGSTHPTS---FTYLNEVADKHGVGCTDIVENRFTGMKSR

Parental  GIYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYTGFWHSPECEFVRHCIAKSQERVEGKV
          GIYETPAGTILYH.HLDIEAFTMD.EV.KIKQGLGLKFAELVYT.FWHSPECEFVRHCIAKS...V.GK.
Retrocopy GIYETPAGTILYHTHLDIEAFTMDWEVCKIKQGLGLKFAELVYTAFWHSPECEFVRHCIAKS*VQVGGKA

Parental  QVSVLKGQVYILGRESPLSLYNEELVSMNVQGDYEPTDATGFININSLRLK--EYHRLQSKVTAK
          QVSVLKGQVYILG.E.PLS.YNEE.VSMNVQGDYEP.DATGFININSLRLK..EYHRLQSKVTAK
Retrocopy QVSVLKGQVYILGWECPLSPYNEEPVSMNVQGDYEPIDATGFININSLRLKE*EYHRLQSKVTAK

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	50.35 RPM
SRP007412_cerebellum	0.00 RPM	33.84 RPM
SRP007412_heart	0.03 RPM	20.98 RPM
SRP007412_kidney	0.12 RPM	925.89 RPM
SRP007412_liver	0.26 RPM	400.50 RPM
SRP007412_testis	1.24 RPM	108.68 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_2403 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2403 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3564
Pan troglodytes	retro_ptro_2421
Pongo abelii	retro_pabe_2937

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020554	3 retrocopies	retro_cjac_1219, retro_cjac_4038, retro_cjac_4209,
Homo sapiens	ENSG00000130707	14 retrocopies	retro_hsap_2247, retro_hsap_2885, retro_hsap_3109, retro_hsap_3175, retro_hsap_3252, retro_hsap_3564, retro_hsap_3824, retro_hsap_4149, retro_hsap_4182, retro_hsap_4648, retro_hsap_4743, retro_hsap_4934, retro_hsap_820, retro_hsap_985,
Gorilla gorilla	ENSGGOG00000010228	8 retrocopies	retro_ggor_1346, retro_ggor_1675, retro_ggor_2134, retro_ggor_2403 , retro_ggor_2574, retro_ggor_2787, retro_ggor_671, retro_ggor_787,
Myotis lucifugus	ENSMLUG00000006066	2 retrocopies	retro_mluc_1058, retro_mluc_1304,
Mus musculus	ENSMUSG00000076441	1 retrocopy	retro_mmus_135,
Nomascus leucogenys	ENSNLEG00000012500	13 retrocopies	retro_nleu_1088, retro_nleu_1245, retro_nleu_1317, retro_nleu_1381, retro_nleu_1390, retro_nleu_1424, retro_nleu_1701, retro_nleu_1792, retro_nleu_220, retro_nleu_253, retro_nleu_2680, retro_nleu_2764, retro_nleu_625,
Pongo abelii	ENSPPYG00000019692	13 retrocopies	retro_pabe_1963, retro_pabe_2390, retro_pabe_2637, retro_pabe_2696, retro_pabe_2937, retro_pabe_3069, retro_pabe_3197, retro_pabe_3422, retro_pabe_3460, retro_pabe_3521, retro_pabe_3522, retro_pabe_731, retro_pabe_834,
Pan troglodytes	ENSPTRG00000021473	14 retrocopies	retro_ptro_1590, retro_ptro_1951, retro_ptro_2101, retro_ptro_2199, retro_ptro_2268, retro_ptro_2421, retro_ptro_2602, retro_ptro_2821, retro_ptro_2836, retro_ptro_3064, retro_ptro_3158, retro_ptro_3298, retro_ptro_571, retro_ptro_762,