RetrogeneDB ID: retro_ggor_1589

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 22:2353006..2353897(+)
• Located in intron of: ENSGGOG00000023698

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSGGOG00000011702
• Aliases: None
• Description: None

Sequence

>retro_ggor_1589
CAGACCCTGGCCTCAGTGCAAGCTCCAGTGCAGACCCCAGCACCCACTCTGCCTGGTCCTGCTCTTCCAGGGCCCTTCCC
TGGTGGCCGTTTGGTCAGGCTGCACCCAGTCATTTTGGCCTCCACTGTGGACAGCTACTAGAGACGCAACAAGGGTGCTG
CCCGAGTTATCGGGACCCTGTTGGGAACTGTCAACAAACACTCAGTGGAGGTCACCAATTGCTTTTCAGTGTCACACAAT
GAGTCAGATGAAGTGGCTGTTGACGTGGAATTTGCTAAGAACATGTATGAACTGCATAAAAAAGTTTCTCCAAATGAGCT
CATCTTGGTGTGGTACGCTGCAGGCCATGACATCACAGAGCACTCTGTGCTGATCCATGAGTACTACAGCCGAGAGGCCC
CCAACCCCATCCACCTCACTGTGGACACAAGTCTCCAGAACGGCCATATGAGCATCGAAGCCTATGTCAGCACTTTAATG
GGTGTCCCTGGGAGGACCGTGGGAGTGTTCACACCTCTGACAGTGAAATATGCATACTATGACACGGAATGCATCAGAGT
TGACCTGATCATGAAGACCTGCTTTAGCCCCAACAGAGTTGTTGGACTCTCAAGTGACTTGCAGCAAGTAGGAGGGGCAT
CAGCTCGCATCCAGGATGCCCTGAGCATAGTGTTGCAATATGCAGAGGATATACTATCTGGAAAGGTGTCAGCTGACAAT
ACCATCAGGAAGGTGGGCCACTTCCTGATGAGCCTGGTTAACCAAGTACCAAAAATAGTTCCCGATGACTTCGAGATCAT
GCTCCACAGCAACATCAATGATCTGTTGATGGTGACCTACCTGGCCAACCTCACACAGTCACAGATTGCCCTCAATGAAA
ATCTTGTAAAC

Alignment

ORF - retro_ggor_1589 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.97 %
• Parental protein coverage: 79.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTPASAQAPAQTPAPALPGPALPGPFPGGRVVRLHPVILASIVDSYERRNEGAARVIGTLLGTVDKHSVE
          QT.AS.QAP.QTPAP.LPGPALPGPFPGGR.VRLHPVILAS.VDSY.RRN.GAARVIGTLLGTV.KHSVE
Retrocopy QTLASVQAPVQTPAPTLPGPALPGPFPGGRLVRLHPVILASTVDSY*RRNKGAARVIGTLLGTVNKHSVE

Parental  VTNCFSVPHNESEDEVAVDMEFAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHL
          VTNCFSV.HNES.DEVAVD.EFAKNMYELHKKVSPNELIL.WYA.GHDITEHSVLIHEYYSREAPNPIHL
Retrocopy VTNCFSVSHNES-DEVAVDVEFAKNMYELHKKVSPNELILVWYAAGHDITEHSVLIHEYYSREAPNPIHL

Parental  TVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQ
          TVDTSLQNG.MSI.AYVSTLMGVPGRT.GV.FTPLTVKYAYYDTE.I.VDLIMKTCFSPNRV.GLSSDLQ
Retrocopy TVDTSLQNGHMSIEAYVSTLMGVPGRTVGV-FTPLTVKYAYYDTECIRVDLIMKTCFSPNRVVGLSSDLQ

Parental  QVGGASARIQDALSTVLQYAEDVLSGKVSADNT---VGRFLMSLVNQVPKIVPDDFETMLNSNINDLLMV
          QVGGASARIQDALS.VLQYAED.LSGKVSADNT...VG.FLMSLVNQVPKIVPDDFE.ML.SNINDLLMV
Retrocopy QVGGASARIQDALSIVLQYAEDILSGKVSADNTIRKVGHFLMSLVNQVPKIVPDDFEIMLHSNINDLLMV

Parental  TYLANLTQSQIALNEKLVN
          TYLANLTQSQIALNE.LVN
Retrocopy TYLANLTQSQIALNENLVN

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	46.61 RPM
SRP007412_cerebellum	0.00 RPM	57.56 RPM
SRP007412_heart	0.00 RPM	45.81 RPM
SRP007412_kidney	0.00 RPM	138.61 RPM
SRP007412_liver	0.00 RPM	109.23 RPM
SRP007412_testis	0.00 RPM	106.60 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_1589 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1589 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Erinaceus europaeus	ENSEEUG00000001226	1 retrocopy	retro_eeur_130,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Homo sapiens	ENSG00000175390	3 retrocopies	retro_hsap_2106, retro_hsap_2512, retro_hsap_4321,
Gorilla gorilla	ENSGGOG00000009774	1 retrocopy	retro_ggor_2235,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589 , retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Oryctolagus cuniculus	ENSOCUG00000004225	1 retrocopy	retro_ocun_1488,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pan troglodytes	ENSPTRG00000003326	1 retrocopy	retro_ptro_197,
Pteropus vampyrus	ENSPVAG00000015764	1 retrocopy	retro_pvam_371,