RetrogeneDB ID: retro_ggor_2

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:22120666..22121779(+)
• Located in intron of: ENSGGOG00000012064

Retrocopy information

• Ensembl ID: ENSGGOG00000034967
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: YY1
• Ensembl ID: ENSGGOG00000026332
• Aliases: None
• Description: None

Sequence

>retro_ggor_2
ATGGCCTCCAACGAAGATTTCTGCATCACAGAAGACCTGGACATCCCGGCAGAGATTGTGGAGCTCCACGACATCAATGT
GGAGCCCCTTCCTATGGAGGACATTCCGACGGAAAGCGTCCAGTACGAGGATGTGGATGGCAATTGGATCTACGGTGGCC
ACAACCATCCGCCTCTGATGGTGCTGCAGCCGCTCTTCACGAACACGGGCTATGGCGACCACGACCAGGAAATGCTTATG
TTGCAGACACAAGAGGAAGTGGTGGGCTATTGCGGCTCAGACAACCAGCTAGGCAACGACTTGGAGGACCAGTTGGCCCT
CCCGGATAGCATTGAAGACGAGCACTTCCAGATGACCCTGGCCTCTCTGTCGGCCTCGGCGGCATCAACATCAACCCAGA
GCCGCAGCAAAAAGCCCAGCAAAAAGCCCAGCGGCAAGAGTGCCACCACCACTGAGGCCAACCCGGCAGGCAGCAGCTCC
AGCGAGGGCACGAGGAAGTGGGAGCAGAAGCAAATGCAGGTCAAAACGCTGGAGGGTGAGTTTTCCGTGACTATGTGGTC
CCCTAACGATAACAATGACCAAGGGGCAGTGGGCGAAGGCCAGGCTGAAAACCCACCTGATTATTCCGAGTACTTGAAAG
GGAAGAAACTTCCTCCTGAGGGGTTACCAGGCATTGATCTCTCAGATCCTAAACAGCTGGCAGAATTTACTAAAGTGAAG
CCCAAAAGGTCCAAAGGAGAACCTCCCAAAACAGTCCCTTGCTCTTATAGCGGCTGCGAAAAGATGTTCAGGGATTACGC
CGCCATGAGAAAACATCTCCACATCCACGGGCCCAGAGTCCACGTATGTGCAGAATGTGGCAAAGCTTTTCTTGAGAGCT
CAAAGCTGAGACGACACCAGCTGGTCCACACCGGCGAGAAGCCCTTTCTGTGCACATTCGAAGGCTGCGGGAAACGCTTT
TCCCTTGATTTCAATTTGCGCACACACTTGCGCATCCACACCGGCGATAAGCCCTTCGTGTGCCCCTTCGATGTTTGCAA
CAGGAAGTTCGCTCAGTCAACCAACCTGAAAACCCATATTTTAACGCATGTGAAGACCAAAAACAGCCCGTGA

Alignment

ORF - retro_ggor_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 65.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DYIEQTLVTVAAAGKSGGGGSSSSGGGRVKKGGGKKSGKKSYLSGGAGAAGGGGADPGNKKWEQKQVQIK
          D.IE........A..S....S.S....R.KK...K.SGK.........A..G.....G..KWEQKQ.Q.K
Retrocopy DSIEDEHFQMTLASLSASAASTSTQS-RSKKPSKKPSGKSATTTEANPA--GSSSSEGTRKWEQKQMQVK

Parental  TLEGEFSVTMWSSDEKKDIDHETVVEEQIIGENSPPDYSEYMTGKKLPPGGIPGIDLSDPKQLAEFARMK
          TLEGEFSVTMWS.......D...V.E.Q......PPDYSEY..GKKLPP.G.PGIDLSDPKQLAEF...K
Retrocopy TLEGEFSVTMWSPNDNN--DQGAVGEGQA---ENPPDYSEYLKGKKLPPEGLPGIDLSDPKQLAEFTKVK

Parental  PRKIKEDDAPRTIACPHKGCTKMFRDNSAMRKHLHTHGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPF
          P...K....P.T..C...GC.KMFRD..AMRKHLH.HGPRVHVCAECGKAF.ESSKL.RHQLVHTGEKPF
Retrocopy PKRSK-GEPPKTVPCSYSGCEKMFRDYAAMRKHLHIHGPRVHVCAECGKAFLESSKLRRHQLVHTGEKPF

Parental  QCTFEGCGKRFSLDFNLRTHVRIHTGDRPYVCPFDGCNKKFAQSTNLKSHILTHAKAKNN
          .CTFEGCGKRFSLDFNLRTH.RIHTGD.P.VCPFD.CN.KFAQSTNLK.HILTH.K.KN.
Retrocopy LCTFEGCGKRFSLDFNLRTHLRIHTGDKPFVCPFDVCNRKFAQSTNLKTHILTHVKTKNS

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	0.96 RPM	17.84 RPM
SRP007412_cerebellum	1.02 RPM	18.87 RPM
SRP007412_heart	0.41 RPM	5.97 RPM
SRP007412_kidney	0.61 RPM	29.32 RPM
SRP007412_liver	0.79 RPM	25.96 RPM
SRP007412_testis	5.59 RPM	44.34 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_2 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_190

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011146	1 retrocopy	retro_amel_2,
Bos taurus	ENSBTAG00000020819	1 retrocopy	retro_btau_91,
Callithrix jacchus	ENSCJAG00000016853	2 retrocopies	retro_cjac_1931, retro_cjac_4045,
Cavia porcellus	ENSCPOG00000020809	2 retrocopies	retro_cpor_1220, retro_cpor_1522,
Equus caballus	ENSECAG00000005805	1 retrocopy	retro_ecab_97,
Homo sapiens	ENSG00000100811	2 retrocopies	retro_hsap_106, retro_hsap_97,
Gorilla gorilla	ENSGGOG00000026332	2 retrocopies	retro_ggor_190, retro_ggor_2 ,
Mustela putorius furo	ENSMPUG00000002931	1 retrocopy	retro_mputfur_867,
Mus musculus	ENSMUSG00000021264	1 retrocopy	retro_mmus_190,
Nomascus leucogenys	ENSNLEG00000000999	3 retrocopies	retro_nleu_1092, retro_nleu_116, retro_nleu_2225,
Oryctolagus cuniculus	ENSOCUG00000026938	1 retrocopy	retro_ocun_1871,
Otolemur garnettii	ENSOGAG00000006955	4 retrocopies	retro_ogar_1231, retro_ogar_1804, retro_ogar_1857, retro_ogar_289,
Pongo abelii	ENSPPYG00000025949	3 retrocopies	retro_pabe_145, retro_pabe_3616, retro_pabe_534,
Pan troglodytes	ENSPTRG00000006717	3 retrocopies	retro_ptro_3093, retro_ptro_45, retro_ptro_494,