RetrogeneDB ID: retro_ggor_1907

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:188228174..188228808(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPS2
• Ensembl ID: ENSGGOG00000001672
• Aliases: None
• Description: None

Sequence

>retro_ggor_1907
AGGCTGCGGGGCGAGAGGGGAGAGGAGGCGGCGGATAAGGTGATGGCGAGAAGATGGAGGAAGAGCAGACGAAGGAAGAG
AAAGGAGATGGAAGAGAGAATGTCACCAGAGGAGACCGAAGGGACACATTTTGACGCTGCAGGAGAAGCTGTGGGCCAGG
CAGAAAGAAAAGGACCAGCTTTTTCTGCAGCTCAAGAAAGTTTCCATGAGGAGGAAAAACGGAGGCGAAAGGAGCAGAGC
GACCTGACCTTCTGACATCCGCTGTGAGCCGGCGGAGCCCGATTATTCACGCGGGGACTCGCTTCCTCCTCGGCATGCAG
GCAGCGCTGGAGGGCACGATCGCCCGGGCATTGTCATAGCAGCTGACCCAGCCAAGCAGATGTTCAGACCCCACGTGCTT
ACGACCCGGAAGTCCGTGGGCTCAGCGGCGGCTTTTGCAGGGACCCCAGAGCAGGCAGCCTGGGCGGTGCCGCTGGGACT
GCTCAGCCCCTACCTCAATATGGGCCCACATAGCTAGCCTATGGCCCTAGTCGGCAGCTCAGAGCAGTTCAGTGCTCCCT
GGGGTGCATTCATGTCCCAGCCACAACCTTATGTTCTGCTGGGCCACTTTCAGCACACCCAGACAGGGTTCCTC

Alignment

ORF - retro_ggor_1907 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.11 %
• Parental protein coverage: 66.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  RERKRQEEEEVDKMMEQKMKEEQERRKKKEMEERMSLEET-KEQILKLEEKLLALQEEKHQLFLQLKKV-
          R.R....EE..DK.M.........RRK.KEMEERMS.EET.K..IL.L.EKL.A.Q.EK.QLFLQLKKV.
Retrocopy RLRGERGEEAADKVMARRWRKSR-RRKRKEMEERMSPEET>KGHILTLQEKLWARQKEKDQLFLQLKKV<

Parental  LHEEEKRRRKEQSDLT-TLTSAAYQQSLTVHTGTH-LLSMQ-GSPGGHNRPGTLMAADRAKQMFGPQVLT
          .HEEEKRRRKEQSDLT..LTSA....S...H.GT..LL.MQ.GS.GGH.RPG...AAD.AKQMF.P.VLT
Retrocopy FHEEEKRRRKEQSDLT<LLTSAVSRRSPIIHAGTRFLLGMQ<GSAGGHDRPGIVIAADPAKQMFRPHVLT

Parental  TRHYVGSAAAFAGTPEH-GQFQGSPGGAYGTAQPPPHYGPTQPAYSPSQQLRA-PSAFPAVQ-YLSQPQP
          TR..VGSAAAFAGTPE..G...G..G....TAQP.P.YGPT..AY.PS.QLRA..S..P.V....SQ..P
Retrocopy TRKSVGSAAAFAGTPEQ<GSLGGAAG----TAQPLPQYGPT*LAYGPSRQLRA<SSVLPGVH<FMSQ--P

Parental  QPYAVHGHFQPTQTGFL
          QPY...GHFQ.TQTGFL
Retrocopy QPYVLLGHFQHTQTGFL

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	1.10 RPM	45.51 RPM
SRP007412_cerebellum	0.39 RPM	41.76 RPM
SRP007412_heart	0.00 RPM	28.17 RPM
SRP007412_kidney	0.00 RPM	61.54 RPM
SRP007412_liver	0.00 RPM	26.25 RPM
SRP007412_testis	0.00 RPM	97.80 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_1907 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1907 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2738
Pan troglodytes	retro_ptro_1852
Macaca mulatta	retro_mmul_1487

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016576	2 retrocopies	retro_amel_1236, retro_amel_362,
Equus caballus	ENSECAG00000010635	2 retrocopies	retro_ecab_124, retro_ecab_480,
Homo sapiens	ENSG00000132522	2 retrocopies	retro_hsap_2738, retro_hsap_4222,
Gorilla gorilla	ENSGGOG00000001672	1 retrocopy	retro_ggor_1907 ,
Macropus eugenii	ENSMEUG00000010645	2 retrocopies	retro_meug_1327, retro_meug_182,
Myotis lucifugus	ENSMLUG00000026169	1 retrocopy	retro_mluc_1045,
Mus musculus	ENSMUSG00000023170	1 retrocopy	retro_mmus_1476,
Nomascus leucogenys	ENSNLEG00000009364	2 retrocopies	retro_nleu_2477, retro_nleu_600,
Pan troglodytes	ENSPTRG00000023046	1 retrocopy	retro_ptro_1852,
Pteropus vampyrus	ENSPVAG00000005052	1 retrocopy	retro_pvam_35,
Sus scrofa	ENSSSCG00000017940	1 retrocopy	retro_sscr_742,