RetrogeneDB ID: retro_ptro_1466

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 21:15078138..15078809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THUMPD1
• Ensembl ID: ENSPTRG00000007848
• Aliases: None
• Description: THUMP domain containing 1 [Source:UniProtKB/TrEMBL;Acc:K7DQV5]

Sequence

>retro_ptro_1466
AGGTGAGGACGCCAACTGCAGTGGAGAAACGTTTCTCTTTCCTCTCAGCTTGCACACATCATGGCGGCTGCTGCCCAGCA
GCCTCCTCAGCCTGGCGGCGGGAAGCACAGAGGCAAGGCTCAGTATGTGCTGGTCAAGCGAGCTCGGCACTGCGAATCTG
GCGGGCCCAGTCAGCCAGAGCCCGGGCTACGGGCATCCTCATCACCTGCAACATGAACCAGCGCAAGTGTGTGGAGGAGG
CTTACACCCTGCTCAACGAATATGGCGATGACATGTATGGGCCAGAAAAGTTTACAGACAAGGATCAGCAGCCCTCTGGA
AGTGAGGGAGAAGATGATGATGTGGAGGCTGTCTTGAAGAAAGAAGTTGGTGACATTGAGGCATCTACAGAGATGAGCCT
AAGAGGATTCCAGTCAGTGGAAAGTGGAGCAAATAACGTCGCCTTCATCAGGACACTTGGGAAAGAACCTGAGAAACTGG
TGCATCATATTCTCCAGGATGAGTACAAAACCAAGAAGACTCAAGTTATTCTACGAATGTTACCCATCTCAGGCACATGC
AAAGCTTTTTTAGAAGATATGAAAAAATATGCAGAAACATTTTTGGAACCCTGGTTTAAAGCTCCAAACAAAGGGACATT
TCAGATTGTGTACAAATCTTGAAATAGCAGT

Alignment

ORF - retro_ptro_1466 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.46 %
• Parental protein coverage: 51.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRGRQQQRRNVSLSSQLAHTMAAPAQQTTQPGGGKRKGKAQYVLAKRARRCDAGGPRQLEPGLQ-GILIT
          R.GRQ.Q.RNVSLSSQLAH.MAA.AQQ..QPGGGK..GKAQYVL.KRAR.C..GGP.Q.EPGL..GILIT
Retrocopy R*GRQLQWRNVSLSSQLAHIMAAAAQQPPQPGGGKHRGKAQYVLVKRARHCESGGPSQPEPGLR<GILIT

Parental  CNMNERKCVEEAYSLLNEYGDDMYGPEKFTDKDQQPSGSEGEDDDAEAALKKEVGDIKASTEMRLRRFQS
          CNMN.RKCVEEAY.LLNEYGDDMYGPEKFTDKDQQPSGSEGEDDD.EA.LKKEVGDI.ASTEM.LR.FQS
Retrocopy CNMNQRKCVEEAYTLLNEYGDDMYGPEKFTDKDQQPSGSEGEDDDVEAVLKKEVGDIEASTEMSLRGFQS

Parental  VESGANNVVFIRTLGIEPEKLVHHILHDMYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWFK
          VESGANNV.FIRTLG.EPEKLVHHIL.D.YKT..KKT.VILRMLPISGTCKAFLEDMKKYAETFLEPWFK
Retrocopy VESGANNVAFIRTLGKEPEKLVHHILQDEYKT--KKTQVILRMLPISGTCKAFLEDMKKYAETFLEPWFK

Parental  APNKGTFQIVYKSRNNS
          APNKGTFQIVYKS.N.S
Retrocopy APNKGTFQIVYKS*NSS

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	0.02 RPM	6.35 RPM
SRP007412_cerebellum	0.00 RPM	12.62 RPM
SRP007412_heart	0.00 RPM	7.93 RPM
SRP007412_kidney	0.00 RPM	14.96 RPM
SRP007412_liver	0.00 RPM	5.14 RPM
SRP007412_testis	0.11 RPM	15.91 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1466 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1466 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1466 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2521
Gorilla gorilla	retro_ggor_1573
Macaca mulatta	retro_mmul_1599

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009499	1 retrocopy	retro_cjac_915,
Cavia porcellus	ENSCPOG00000008919	1 retrocopy	retro_cpor_71,
Felis catus	ENSFCAG00000015158	1 retrocopy	retro_fcat_195,
Homo sapiens	ENSG00000066654	1 retrocopy	retro_hsap_2521,
Gorilla gorilla	ENSGGOG00000005231	1 retrocopy	retro_ggor_1573,
Macaca mulatta	ENSMMUG00000004225	1 retrocopy	retro_mmul_1599,
Monodelphis domestica	ENSMODG00000006971	1 retrocopy	retro_mdom_54,
Nomascus leucogenys	ENSNLEG00000012369	1 retrocopy	retro_nleu_1443,
Pan troglodytes	ENSPTRG00000007848	1 retrocopy	retro_ptro_1466 ,