RetrogeneDB ID: retro_ggor_1573

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 21:17170898..17171572(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THUMPD1
• Ensembl ID: ENSGGOG00000005231
• Aliases: None
• Description: None

Sequence

>retro_ggor_1573
GGGAGGTGAGGACGCCAACTGCAGTGGAGAAACTTTTCTCTTTCCTCTCAGCTTGCACACATCATGGCGGCTGCTGCCCA
GCAGCCTCCTCAGCCTGGCGGCGGGAAGCACAGAGGCAAGGCTCAGTATGTGCTGGTCAAGCGAGCTCGGCACTGCGAAT
CTGGCGGGCCCAGTCAGCCAGAGCCCAGGCTACGGGCATCCTCATCACCTGCAACATGAACCAGCGCGAGTGTGTGGAGG
AGGCTTACACCCTGCTCAACGAATATGGCGATGACATGTACGGGCCAGAAAAGTTTACAGACAAGGATCAGCAGCCCTCT
GGAAGTGAGGGAGAAGATGATGATGTGGAGGCTGTCTTGAAGAAAGAAGTTGGTGACATTAAGGCATCTACAGAGATGAG
CCTAAGAGGATTCCAGTCAGTGGAAAGTGGAGCAAATAACGTCGTCTTCATCAGGACACTTGGGAAAGAACCTGAGAAAT
TGGTGCATCATATTCTCCAGGATGAGTACAAAACCAAGAAGACTCAAGTTATTCTACGAATATTACCCATCTCAGGCACA
TGCAAAGTTTTTTTAGAAGATATGAAAAAATATGCAGAAACATTTTTGGAACCCTGGTTTAAAGGTCCAAACAAAGGGAC
ATTTCAGATTGTGTACAAATCTTGAAATAGCAGT

Alignment

ORF - retro_ggor_1573 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.02 %
• Parental protein coverage: 59.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRGGRQQQRRNVSLSSQLAHTMAAPAQQATQPGGGKRKGKAQYVLAKRARRCDAGGPRQLEPGLQ-GILI
          GR.GRQ.Q.RN.SLSSQLAH.MAA.AQQ..QPGGGK..GKAQYVL.KRAR.C..GGP.Q.EP.L..GILI
Retrocopy GR*GRQLQWRNFSLSSQLAHIMAAAAQQPPQPGGGKHRGKAQYVLVKRARHCESGGPSQPEPRLR<GILI

Parental  TCNMNERKCVEEAYSLLNEYGDDMYGPEKFTDKDQQPSGSEGEEDDAEAALKKEVGDIKASTEMRLRRFQ
          TCNMN.R.CVEEAY.LLNEYGDDMYGPEKFTDKDQQPSGSEGE.DD.EA.LKKEVGDIKASTEM.LR.FQ
Retrocopy TCNMNQRECVEEAYTLLNEYGDDMYGPEKFTDKDQQPSGSEGEDDDVEAVLKKEVGDIKASTEMSLRGFQ

Parental  SVESGANNVVFIRTLGIGKKXLVHHILQDMYKTKKKKTRVILRMLPISGTCKAFLEDMKKYAETFLEPWF
          SVESGANNVVFIRTLG.....LVHHILQD.YKT..KKT.VILR.LPISGTCK.FLEDMKKYAETFLEPWF
Retrocopy SVESGANNVVFIRTLGKEPEKLVHHILQDEYKT--KKTQVILRILPISGTCKVFLEDMKKYAETFLEPWF

Parental  KAPNKGTFQIVYKSRNNS
          K.PNKGTFQIVYKS.N.S
Retrocopy KGPNKGTFQIVYKS*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	0.29 RPM	12.95 RPM
SRP007412_cerebellum	0.08 RPM	8.31 RPM
SRP007412_heart	0.09 RPM	2.22 RPM
SRP007412_kidney	0.04 RPM	11.04 RPM
SRP007412_liver	0.08 RPM	5.43 RPM
SRP007412_testis	0.31 RPM	29.22 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_1573 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1573 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2521
Pan troglodytes	retro_ptro_1466
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,