RetrogeneDB ID: retro_ptro_2901

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:80723712..80725318(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX10
• Ensembl ID: ENSPTRG00000004256
• Aliases: None
• Description: None

Sequence

>retro_ptro_2901
ATGGGCAAAACTGCGGACTCTCCGGGTTCGGGAGCCCGACCCGACCCGGTACGGAGCTTCAATCGCTGGAAGAAAAAACA
CAGCCACGGGCAGAACAAAAAGAATCAGTTGAGGAAGCAACTGAAGAAACCCGAATGGCAGGTCGAGCGCAAGGGTAACA
GCCGCCTCATGCAGAACTATGAGAAGATAAATGTAAATGAAATTACAAGATTTTCAGATTTTTCCTTGTCCAAAAAAACA
CTGAAAGGTTTGCAAGAAGCTCAGTACCGTTTGGTAACTGAGATACAGAAGCAGACCATTGGATTGGCTTTGCAAGGTAG
AGATGTACCTGGAGTGGCCAAAACTGGATCTGGCAAGACTTTAGCTTTCCTTGTTCCAGTGCTAGAAGCCTTATATCGTC
TGCAATAGACCTCAACAGATGGGCTGGGGGTTCTCATAATATCACCTATGAGAGAACTGACCTATCAGACCTTTGAGGTT
CTCCAAAAGGTAGGAAAGAATCATGACTTCTCAGCTGGTCTCATCATTGGTGGAAAGTATCTGAAACACGAAGCTGAGAG
GATCAACAACATAAATATACTCGTGTGCGCACCAGGTCGGCTTCTTCAACACATGGATGAAACGGTGTCTTTTCATGCTA
CTGCTCTCCTAATGTTAGTTCTTGATGAAGCATATAGAATCTTGGATGTGGGCCTTGCTGATACCATGAATGCTATTATT
GAAAATCTCCCCAAGAAACGTCAGACTTTACTTTTCTCAGCAACACAAACTATATCTGTAAAGGACCTTGCACGCTTGAG
TTTGAAAAACACTGAGTATGTCTGGGTTCATGAAAAATGCAAAATATAGCACCCCTGCCACTTTGGAACAGAACTACATA
GTCTGTGAGCAGCAGCAAAAAATAAGTGTGCTGTATTCCTTTTTGAGAAGGCACCTGAAGAAGAAGAGCATTGTATTTTT
TTCCAGTTGCTAAAAGGTCTGATATCTGTACCGAGTGTTTTGCCAGCTACGTCCTGGTATTTCTATCCTTGCCCTCCATG
GTCGATAGCAGCAAATGAGAAGAATGGAAGTCTATAATGAGTTTGTCCGTAAGACAGCTGCAGTACTCTTTGCTAGTGAT
GTTGCAGCCAGGGGGCTGGATTTCCCGGCTGTGAATTGGGCTCTTCAGTTTGATTGTCCTGAGGATGCCAACACATATAT
TCACAGAGCAGGTAGAACTGCTAGGTACAAAGAGGATGGTGAAGCTTTATTAATTTTGCTTGCCTCAGAAAAAGCTATAG
TGCAGCAGCTTCTTCAGAAGAAAGTACCTATAAAGGAAATCAAAATCAATCCAGAAAAACTTACAGATATCCAGAAAAAA
TTGGAATCTTTTTTAGCTGAAGATCAAGATTTAAAAGAAAGAGCTCAAAGGTGTTTCGTCTCCGATATATGATTGGTATA
TCTGATGAAGGATAAAGAAGTATTTGATGTGAGCAAGTTACCTATACCTGAATATGCCCTGTCTCTTGGGCTTGCTGTGG
CACCATGCATAAGATTTCTTCAGAAAATGCAGAAACAACCCACCAAAGAATTGGTAATGAGCCAAGCCAATAAAGTAACT
GAGCCA

Alignment

ORF - retro_ptro_2901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.3 %
• Parental protein coverage: 61.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGKTADSPGSGARPDPVRNFNRWKKKHSHRQNKKKQLRKQLKKPEWQVERESISRLMQNYEKINVNEITR
          MGKTADSPGSGARPDPVR.FNRWKKKHSH.QNKK.QLRKQLKKPEWQVER...SRLMQNYEKINVNEITR
Retrocopy MGKTADSPGSGARPDPVRSFNRWKKKHSHGQNKKNQLRKQLKKPEWQVERKGNSRLMQNYEKINVNEITR

Parental  FSDFPLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQWTSTD
          FSDF.LSKKTLKGLQEAQYRLVTEIQKQTIGLALQG.DV.G.AKTGSGKTLAFLVPVLEALYRLQ.TSTD
Retrocopy FSDFSLSKKTLKGLQEAQYRLVTEIQKQTIGLALQGRDVPGVAKTGSGKTLAFLVPVLEALYRLQ*TSTD

Parental  GLGVLIISPTRELAYQTFEVLRKVGKNHDFSAGLIIGGKDLKHEAERINNINILVCTPGRLLQHMDETVS
          GLGVLIISP.REL.YQTFEVL.KVGKNHDFSAGLIIGGK.LKHEAERINNINILVC.PGRLLQHMDETVS
Retrocopy GLGVLIISPMRELTYQTFEVLQKVGKNHDFSAGLIIGGKYLKHEAERINNINILVCAPGRLLQHMDETVS

Parental  FHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK-
          FHAT.L.MLVLDEA.RILD.G.ADTMNA.IENLPKKRQTLLFSATQT.SVKDLARLSLKN.EYVWVHEK.
Retrocopy FHATALLMLVLDEAYRILDVGLADTMNAIIENLPKKRQTLLFSATQTISVKDLARLSLKNTEYVWVHEK>

Parental  AKYSTPATLEQNYIVCELKQKISVLYSFLRSHLKKKSIVFFSSCKEVQYLYRVFCRLRPGVSILALHGRQ
          AKYSTPATLEQNYIVCE..QKISVLYSFLR.HLKKKSIVFFSSC..V.YLYRVFC.LRPG.SILALHGR.
Retrocopy AKYSTPATLEQNYIVCEQQQKISVLYSFLRRHLKKKSIVFFSSC*KV*YLYRVFCQLRPGISILALHGR*

Parental  QQMRRMEVYNEFVRKRAAVLFATDIAARGLDFPAVNWVLQFDCPEDANTYIHRAGRTARYKEDGEALLIL
          QQMRRMEVYNEFVRK.AAVLFA.D.AARGLDFPAVNW.LQFDCPEDANTYIHRAGRTARYKEDGEALLIL
Retrocopy QQMRRMEVYNEFVRKTAAVLFASDVAARGLDFPAVNWALQFDCPEDANTYIHRAGRTARYKEDGEALLIL

Parental  LPSEKAMVQQLLQKKVPVKEIKINPEKLIDVQKKLESILAQDQDLKERAQRCFVSYVRSVYLMKDKEVFD
          L.SEKA.VQQLLQKKVP.KEIKINPEKL.D.QKKLES.LA.DQDLKERAQRCFVS....VYLMKDKEVFD
Retrocopy LASEKAIVQQLLQKKVPIKEIKINPEKLTDIQKKLESFLAEDQDLKERAQRCFVSDI*LVYLMKDKEVFD

Parental  VSKLPIPEYALSLGLAVAPRIRFLQKMQKQPTKELVMSQADKVIEP
          VSKLPIPEYALSLGLAVAP.IRFLQKMQKQPTKELVMSQA.KV.EP
Retrocopy VSKLPIPEYALSLGLAVAPCIRFLQKMQKQPTKELVMSQANKVTEP

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	14.82 RPM
SRP007412_cerebellum	0.00 RPM	18.82 RPM
SRP007412_heart	0.00 RPM	9.65 RPM
SRP007412_kidney	0.03 RPM	22.23 RPM
SRP007412_liver	0.00 RPM	18.10 RPM
SRP007412_testis	0.11 RPM	72.50 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2901 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2901 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2901 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4278
Gorilla gorilla	retro_ggor_2862

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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 ,