RetrogeneDB ID: retro_ggor_1840

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:33650885..33651858(+)
• Located in intron of: ENSGGOG00000000171

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUGT1
• Ensembl ID: ENSGGOG00000006797
• Aliases: None
• Description: None

Sequence

>retro_ggor_1840
GTGGCAGCTGCAGCAGGACCTGCAACTTCCCAGAGGTTTTTCCAGAGCTTCTTGGATACTCTAATCGACGAGGACCCCCA
GGCGGCATTAGAGGAGCTGACTAAGGCTTTGGAACAGAAACCAAATGATGCATAATATTAGTGTCAAAGAGCTTATTGTC
ACATTCTTCTTGGTAATTACTGTGTTGCTGTTGCTGATGGAAAGAAGTCTCTCGAATTCAATCCAAATAATTCCACCACT
ATGTTGAGAAAAGGAACATGTGAATACTATGAAAAAAACTATGTTGCTGCCCTAGAAATTTTTACAGAAGGACAAAAATT
AGTGCAGATGCTAATTTCAGTGTCTGGATTAAAAGATGTCAAGAAGCTCAGAATGGCCCAGAATCTGAGGTGTGGACTCA
TCAGTGAAAAATCAGGTATGACTGGTATCAAACAGAATCGCAAGTAGTCATTACACTTATGATCAAGAATGTTCAAAGAA
TGATGTAAATGTGGAATTTTCAGAAAAGGAATTGTCTGCTTTGGTTAAACTTCCTTTGGAGAGGATTACAATTTGAAACT
GGAACTTCATCCTATAATACCAGAACAGAGGACATTTAAAGTAGTTTCAACCAAGATTGAAATTAAACTGAAAAAGCCAG
AGGCTGTGAGATGGGAAAAGCTAGAGGGGCAAGGAGATGTGCCTACACCAAAACAATTCATAGCAGGTGTAAAGCACCTA
CATCCATCATCATCTCCTTATACAAGAAATTGGGATAAATTAGTGGGTAAAATCAAAGAAGAAGAAAATAATGAAAAGTT
GGAGGGAGATGCAGCTTTAAACAGATTATTTCAGCAGATCTATTCAGATGGTTCTGATGAAGTGAAATGTGCCATGAACA
GATGCTTTATGGGAGTCTGATGGTACAGTTTTGAGTACCAGCTGGTCTGATGTAGGTAAAAGGAAAGTTGAAATCAATCC
TGATGATATGGAA

Alignment

ORF - retro_ggor_1840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.24 %
• Parental protein coverage: 98.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VASWGRTATSQRFFQSFSDALIDEDPQAALEELTKALEQKPDDAQYYCQRAYCHILLGNYCVAVADAKKS
          VA.....ATSQRFFQSF.D.LIDEDPQAALEELTKALEQKP.DA.Y.CQRAYCHILLGNYCVAVAD.KKS
Retrocopy VAAAAGPATSQRFFQSFLDTLIDEDPQAALEELTKALEQKPNDA*Y*CQRAYCHILLGNYCVAVADGKKS

Parental  LELNPNNSTAMLRKGICEYHGKNYAAALE-TFTEGQKLDSADANFSVWIKRCQEAQNGSESEVWTHQSKI
          LE.NPNNST.MLRKG.CEY..KNY.AALE..F....K..SADANFSVWIKRCQEAQNG.ESEVWTHQ.KI
Retrocopy LEFNPNNSTTMLRKGTCEYYEKNYVAALE<NFYRRTKI-SADANFSVWIKRCQEAQNGPESEVWTHQ*KI

Parental  KYDWYQTESQVVITLMIKNVQ-KNDVNVEFSEKELSALVKLPS-GEDYNLKLELLHPIIPEQSTFKVLST
          .YDWYQTESQVVITLMIKNVQ.KNDVNVEFSEKELSALVKLP..GEDYNLKLEL.HPIIPEQ.TFKV.ST
Retrocopy RYDWYQTESQVVITLMIKNVQ<KNDVNVEFSEKELSALVKLPL<GEDYNLKLEL-HPIIPEQRTFKVVST

Parental  KIEIKLKKPEAVRWEKLEGQGDVPTPKQFVADVKNLYPSSSPHTRNWDKLVGEIREEEKNEKLEGDAALN
          KIEIKLKKPEAVRWEKLEGQGDVPTPKQF.A.VK.L.PSSSP.TRNWDKLVG.I.EEE.NEKLEGDAALN
Retrocopy KIEIKLKKPEAVRWEKLEGQGDVPTPKQFIAGVKHLHPSSSPYTRNWDKLVGKIKEEENNEKLEGDAALN

Parental  RLFQQIYSDGSDEVKRAMNKSFM-ESGGTVLSTNWSDVGKRKVEINPPDDME
          RLFQQIYSDGSDEVK.AMN..FM.ES.GTVLST.WSDVGKRKVEIN.PDDME
Retrocopy RLFQQIYSDGSDEVKCAMNRCFM>ESDGTVLSTSWSDVGKRKVEIN-PDDME

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	13.04 RPM
SRP007412_cerebellum	0.28 RPM	9.10 RPM
SRP007412_heart	0.09 RPM	5.47 RPM
SRP007412_kidney	0.29 RPM	21.59 RPM
SRP007412_liver	0.16 RPM	14.56 RPM
SRP007412_testis	0.41 RPM	36.36 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_1840 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1840 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2628
Pan troglodytes	retro_ptro_1773

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008606	2 retrocopies	retro_amel_353, retro_amel_896,
Canis familiaris	ENSCAFG00000004823	1 retrocopy	retro_cfam_136,
Callithrix jacchus	ENSCJAG00000003604	1 retrocopy	retro_cjac_310,
Cavia porcellus	ENSCPOG00000003374	1 retrocopy	retro_cpor_110,
Dasypus novemcinctus	ENSDNOG00000002991	1 retrocopy	retro_dnov_2621,
Homo sapiens	ENSG00000165416	1 retrocopy	retro_hsap_2628,
Gorilla gorilla	ENSGGOG00000006797	1 retrocopy	retro_ggor_1840 ,
Nomascus leucogenys	ENSNLEG00000015700	1 retrocopy	retro_nleu_640,
Otolemur garnettii	ENSOGAG00000008220	1 retrocopy	retro_ogar_41,
Pan troglodytes	ENSPTRG00000005906	1 retrocopy	retro_ptro_1773,