RetrogeneDB ID: retro_ggor_581

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 10:62819235..62820949(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHQ1
• Ensembl ID: ENSGGOG00000034818
• Aliases: None
• Description: None

Sequence

>retro_ggor_581
ATGCTGACCCCAGCGTTCAGCCTCAGCCAGGAGCCGGATTTCCTGACCATCGCCATCCGCGTGCCCTACGCCCCGGCCTC
CGAGTTCAACGTCTACTTCGAGGGGTCGGCCTAGACTACTATGCCAAGCCGTACTTTCTCAGATTAACCCCTCCTGGAAG
AATTGTAGAATATGGAAGCGAGCAAGGGTCCTATGATGCAGATAAAGGAATTTTTACCACTCGCCTGCCCAAAGAAACCC
CTGGCCAGCATTTTGAGGGGCTGAACATGTGTTGCTCTTCTGGCACCAGGAAAATCCGGGACAGCAAAACCACTTGTGGA
AGCAATAGGTGATTCTGAAATTCCTGAGGAAGTAGTTCACGATGAAGAGTTTGATTGGGAAATTGAGCAGACACCCTATG
AAGAGGTAACAGAAAGTGCTTTGAATCCTCATGCTACTATGGGTTTGGAAACTTACGATCAGGAGTGTTTCAGCAGTTAC
AGGATGAATTGAGTGATGTTATTAAGGATCCAGATTTCACCCCTGCAGCAGAACGAAAACAAAAGCACCTGGCCGCTGAG
CTGGCCAAGTTTGATCCTGATCATTATCTAGCTGACTTTTTGGAAGATGAGGCAGTTGAACAGATTTTGAAGTATAATCC
TTGGTGGACTGACAAATATTAAAAAACGACGGCCTTTTTGGAAAAGAGTCAGAAGCAAGAAAATCATGCTGCATTAGTGT
CTTTTTCTGAAGAAGAGAAATATCAGCTACAAGAATTTGTCGATAAATCTTATCTGCTAGACAACAGAGCCTGTCGTCAA
GTGTGCTACAGTTCGATTGATATCCTTCTGGCATATTGCTAAGAAACCCGTGTCACTGAAGGACAGAAGAACGTTGAATC
TGCATGGAATATCAGGAAACTGAGTCCAATACTATGCTGGTTTGAGACTTGGACTAATGTTCATGATATCATGGTGTCTT
TTGGAAGAAGGGTATTGTGTTACCCGCTCTATCGCCATTTCAAACTGGCGATGAAGGCCTACGGGGAGACTATAAAGATA
CTGCAACTAGGTAAAAGTGCAGTTTTAAAGTGTCTCCTGGATATTCACAAATTTTTTCAGGAAAACGACCCAGCATACAT
ATTGAATGATCTCTACATCTCAGACTACTGTGTGTGGATTCAGAAAGTCAAATCCAAAACGTTGGCAGCTCTTGCAGAAG
CCTTAAAGGAAGTCTCCCTTACAAAGGCCCAGTTGGGGTGAGAACTGGAAGAACTAGAAGCAGCAGCACTTCTTGTCCAG
GAGGAAGAATCTGCATTACAAGCAGCCCATTCAGTTTCTGGGCAGCAGAAACTTTGCTGCAGCTCTGAGGCAGGTGATTC
AGAGGACTCAGACAGCACTGTGTCATCTGGAAACGAAGACTCAGACTCGCATTCAGAACAAGATGAACTCAAAGATAGTC
CATCTGAGACAGTTCTTTGCAAGGTCCCCTTCTTGAAGAAAGCAGTGCCCTTCTGATTGTTGATGGTGGAGTATGCAGAA
ACACAGCCATCCAGGAGTCTGATGCCAGTCAGGGAAAGCCACTTGCCTCTTCCCGGCCTCTTGGAGTGTCTGGGCCTCTG
ATAGAGGAGCTTGGGGAACAACTGAAGACCACCGTTCAGGTTTTTGAACCCGAGGGCACCACTGCTGTAGACCACAGCAA
CATGCAGGAGAGAGATGGCTGTCAGACACCAAAT

Alignment

ORF - retro_ggor_581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.34 %
• Parental protein coverage: 99.83 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MLTPAFDLSQDPDFLTIAIRVPYARVSEFDVYFEGS-DFKFYAKPYFLRLTLPGRIVENGSEQGSYDADK
          MLTPAF.LSQ.PDFLTIAIRVPYA..SEF.VYFEGS.....YAKPYFLRLT.PGRIVE.GSEQGSYDADK
Retrocopy MLTPAFSLSQEPDFLTIAIRVPYAPASEFNVYFEGS<GLDYYAKPYFLRLTPPGRIVEYGSEQGSYDADK

Parental  GIFTIRL-PKETPGQHFEGLNMLTALLAPRKSRTAKPLVEEIVASEIPEEVVDDEEFDWEIEQTPYEEVS
          GIFT.RL.PK........G.....ALLAP.KS.TAKPLVE.I..SEIPEEVV.DEEFDWEIEQTPYEEV.
Retrocopy GIFTTRL>PKKPLASILRG*TCV-ALLAPGKSGTAKPLVEAIGDSEIPEEVVHDEEFDWEIEQTPYEEVT

Parental  ESALNPQ-CHYGFGNLRSGVLQRLQDELSDVVDIKDPDFTPAAERRQKRLATELAKFDPDHYLADFFEDE
          ESALNP..C.YGFGNLRSGV.Q.LQDELSDV..IKDPDFTPAAER.QK.LA.ELAKFDPDHYLADF.EDE
Retrocopy ESALNPH<CYYGFGNLRSGVFQQLQDELSDV--IKDPDFTPAAERKQKHLAAELAKFDPDHYLADFLEDE

Parental  AIEQILKYNPWWTDKYSKMTAFLEKSQEQENHATLVSFSEEEKYQLRKFVNKSYLLDKRACRQVCYSLID
          A.EQILKYNPWWTDKY.K.TAFLEKSQ.QENHA.LVSFSEEEKYQL..FV.KSYLLD.RACRQVCYS.ID
Retrocopy AVEQILKYNPWWTDKY*KTTAFLEKSQKQENHAALVSFSEEEKYQLQEFVDKSYLLDNRACRQVCYSSID

Parental  ILLAYCYETRVTEGEKNVESAWNIRKLSPTLCWFETWTNVHDIVVSFGRRVLCYPLYRHFKLVMKAYRDT
          ILLAYC.ETRVTEG.KNVESAWNIRKLSP.LCWFETWTNVHDI.VSFGRRVLCYPLYRHFKL.MKAY..T
Retrocopy ILLAYC*ETRVTEGQKNVESAWNIRKLSPILCWFETWTNVHDIMVSFGRRVLCYPLYRHFKLAMKAYGET

Parental  IKILQLGKSAVLKCLLDIHKIFQENDPAYILNDLYISDYCVWIQKVKSKKLAALAEALKEVSLTKAQLGL
          IKILQLGKSAVLKCLLDIHK.FQENDPAYILNDLYISDYCVWIQKVKSK.LAALAEALKEVSLTKAQLG.
Retrocopy IKILQLGKSAVLKCLLDIHKFFQENDPAYILNDLYISDYCVWIQKVKSKTLAALAEALKEVSLTKAQLG*

Parental  ELEELEAAALLVQEEETALKAAHSVSGQQTLCSSSEASDSEDSDSTVSSGNEDSGSDSEQDELKDSPSET
          ELEELEAAALLVQEEE.AL.AAHSVSGQQ.LC.SSEA.DSEDSDSTVSSGNEDS.S.SEQDELKDSPSET
Retrocopy ELEELEAAALLVQEEESALQAAHSVSGQQKLCCSSEAGDSEDSDSTVSSGNEDSDSHSEQDELKDSPSET

Parental  VNSLQGPF-LEESSALLIVDGGVRRNTAIQESDASQGKPLSSSWPLGVSGPLIEELGEQLKTTVQVSEPK
          V.....PF.LEESSALLIVDGGV.RNTAIQESDASQGKPL.SS.PLGVSGPLIEELGEQLKTTVQV.EP.
Retrocopy V-LCKVPF<LEESSALLIVDGGVCRNTAIQESDASQGKPLASSRPLGVSGPLIEELGEQLKTTVQVFEPE

Parental  GTTAVNRSNMQERDGCQTPN
          GTTAV..SNMQERDGCQTPN
Retrocopy GTTAVDHSNMQERDGCQTPN

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	0.48 RPM	8.20 RPM
SRP007412_cerebellum	0.35 RPM	7.92 RPM
SRP007412_heart	0.16 RPM	2.53 RPM
SRP007412_kidney	1.51 RPM	14.88 RPM
SRP007412_liver	1.29 RPM	9.63 RPM
SRP007412_testis	3.83 RPM	20.72 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_581 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_581 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_674
Pan troglodytes	retro_ptro_486

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015131	1 retrocopy	retro_cjac_1045,
Homo sapiens	ENSG00000144736	1 retrocopy	retro_hsap_674,
Gorilla gorilla	ENSGGOG00000034818	1 retrocopy	retro_ggor_581 ,
Nomascus leucogenys	ENSNLEG00000002731	1 retrocopy	retro_nleu_463,
Pongo abelii	ENSPPYG00000013717	1 retrocopy	retro_pabe_546,
Pan troglodytes	ENSPTRG00000015106	1 retrocopy	retro_ptro_486,