RetrogeneDB ID: retro_ggor_2862

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 9:63966266..63967686(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX10
• Ensembl ID: ENSGGOG00000000271
• Aliases: None
• Description: None

Sequence

>retro_ggor_2862
ATAAATGTAAATGAAATTACAAGATTTTCAGATTTTTCCTTGTCCAAAAAAACATTGAAAGGTTTGCAAGAAGCTCAGTA
CGGTTTGGTAACTGAGATACAGAAGCAGACCATTGGATTGGCTTTGCAAGGTAGAGATGTACCTGGAGTGGCCAAAACTG
GATCTGGCAAGACTTTGGCTTTCCTTGTTCCAGTGCTAGAAGCCTTATATCGTCTGCAATAGACCTCAACAGATGGGCTG
GGGGTTCTCATAATATCACCTATGAGAGAACTGGCCTATCAGACCTTTGAGGTTCTCCAAAAGGTAGGAAAGAATCATGA
CTTCTCAGCTGGTCTCATCATTGGTGGAAAGTATCTGAAACACGAAGCTGAGAGGATCAACAACATAAATATACTCGTGT
GTGCATCAGGTCGGCTTCTTCAACACCTGGATGAAACGGTGTCTTTTCATGCCACTGCTCTCCTAATGTTAGTTCTTGAT
GAAGCATATAGTATCTTGGATGTGGGCTTTGCTGATACCATGAATGCTATTATTGAAAATCTCCCCAAGAAACGTCAGAC
TTTACTTTTCTCAGCAACGCAAACTATATCTGTAAAGGACCTTGCACACCTGAGTTTGAAAAACACTGAGTATGTCTGGG
TTCATGAAAAATGCAAAATATAGCACCCCTGCCACTTTGGAACAGAACTACATAGTCTGTGAGCAGCAGCAAAAAAGAAG
TGTGCTGTATTCCTTTTTGAGAAGGCACCTGAAGAAGAAGAGCATTGTATTTTTTTCTAGTTGCAAAAAGATCTGATATC
TGTACCAAGTGTTTTGCCAGCTACGTCATGGTATTTCTATCCTTGCCCTCCATGGTTGATAGCAGCAAATGAGAAGAATG
GAAGTCTATAATGAGTTTGTCCGTAAGAGAGCTGCAGTACTCTTTGCTAGTGATGTTGCAGCCAGGGGGCTGGATTTCCT
GGCTGTGAATTGGGCTCTTCAGTTTGATTGTCCTGAGGATGCCAACACATATATTCACAGAGCAGGTAGAACTGCCAGGT
ACAAAGAGGATGGTGAAGCTTTATTAATTTTGCTTGCCTCAGAAAAAGCTATAGTGCAGCAGCTTCTTCAGAAGAAAGTA
CCTATAAAGGAAATCAAAATCAATCCAGAAAAACTTATAGATATCCAGAAAAAATTGGAATCTTTTTTAGCTGAAGATCA
AGATTTAAAAGAAAGAGCTCAAAGGTGTTTCATCTCCGATATATGATTGGTGTATCTGATGAAGGATAAAGAAGTATTTG
ATGTGAGCAAGTTACCTATACCTGAATATGCCCTGTCTCTTGGGCTTGCTGTGGCACCATGCATAAGATTTCTTCAGAAA
ATGCAGAAACAACCCACCAAAGAATTGGTAATGAGCCAAGCCAATAAAGTAACTGAGCCA

Alignment

ORF - retro_ggor_2862 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.82 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INVNEITRFSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALY
          INVNEITRFSDF.LSKKTLKGLQEAQY.LVTEIQKQTIGLALQG.DV.G.AKTGSGKTLAFLVPVLEALY
Retrocopy INVNEITRFSDFSLSKKTLKGLQEAQYGLVTEIQKQTIGLALQGRDVPGVAKTGSGKTLAFLVPVLEALY

Parental  RLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLL
          RLQ.TSTDGLGVLIISP.RELAYQTFEVL.KVGKNHDFSAGLIIGGK.LKHEAERINNINILVC..GRLL
Retrocopy RLQ*TSTDGLGVLIISPMRELAYQTFEVLQKVGKNHDFSAGLIIGGKYLKHEAERINNINILVCASGRLL

Parental  QHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPE
          QH.DETVSFHAT.L.MLVLDEA..ILD.GFADTMNA.IENLPKKRQTLLFSATQT.SVKDLA.LSLKN.E
Retrocopy QHLDETVSFHATALLMLVLDEAYSILDVGFADTMNAIIENLPKKRQTLLFSATQTISVKDLAHLSLKNTE

Parental  YVWVHEK-AKYSTPATLEQNYIVCELKQKISVLYSFLRSHLKKKSIVFFSSCKEVQYLYRVFCRLRPGVS
          YVWVHEK.AKYSTPATLEQNYIVCE..QK.SVLYSFLR.HLKKKSIVFFSSCK...YLY.VFC.LR.G.S
Retrocopy YVWVHEK>AKYSTPATLEQNYIVCEQQQKRSVLYSFLRRHLKKKSIVFFSSCKKI*YLYQVFCQLRHGIS

Parental  ILALHGRQQQMRRMEVYNEFVRKRAAVLFATDIAARGLDFPAVNWVLQFDCPEDANTYIHRAGRTARYKE
          ILALHG..QQMRRMEVYNEFVRKRAAVLFA.D.AARGLDF.AVNW.LQFDCPEDANTYIHRAGRTARYKE
Retrocopy ILALHG**QQMRRMEVYNEFVRKRAAVLFASDVAARGLDFLAVNWALQFDCPEDANTYIHRAGRTARYKE

Parental  DGEALLILLPSEKAMVQQLLQKKVPVKEIKINPEKLIDVQKKLESILAQDQDLKERAQRCFVSYVRSVYL
          DGEALLILL.SEKA.VQQLLQKKVP.KEIKINPEKLID.QKKLES.LA.DQDLKERAQRCF.S....VYL
Retrocopy DGEALLILLASEKAIVQQLLQKKVPIKEIKINPEKLIDIQKKLESFLAEDQDLKERAQRCFISDI*LVYL

Parental  MKDKEVFDVSKLPIPEYALSLGLAVAPRIRFLQKMQKQPTKELVMSQADKVIEP
          MKDKEVFDVSKLPIPEYALSLGLAVAP.IRFLQKMQKQPTKELVMSQA.KV.EP
Retrocopy MKDKEVFDVSKLPIPEYALSLGLAVAPCIRFLQKMQKQPTKELVMSQANKVTEP

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	15.54 RPM
SRP007412_cerebellum	0.00 RPM	9.93 RPM
SRP007412_heart	0.00 RPM	3.47 RPM
SRP007412_kidney	0.04 RPM	21.88 RPM
SRP007412_liver	0.00 RPM	8.34 RPM
SRP007412_testis	0.10 RPM	46.00 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_2862 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2862 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4278
Pan troglodytes	retro_ptro_2901

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000178105	1 retrocopy	retro_hsap_4278,
Gorilla gorilla	ENSGGOG00000000271	1 retrocopy	retro_ggor_2862 ,
Pongo abelii	ENSPPYG00000003849	1 retrocopy	retro_pabe_3489,
Pan troglodytes	ENSPTRG00000004256	1 retrocopy	retro_ptro_2901,