RetrogeneDB ID: retro_ggor_1850

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 3:53712403..53713879(+)
• Located in intron of: ENSGGOG00000015852

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENSG00000078304
• Ensembl ID: ENSGGOG00000010878
• Aliases: None
• Description: None

Sequence

>retro_ggor_1850
AAAGAATCACCAAAAGCAGGGAAGAGTGGAAAAAGTTCAAAAGAAGGACAAGACACAGTAGAATCAGAGCAAATTTCCGT
CAGGAAAAACAGCCTTGTTGCTGTCCCGTCTACAGTGTCTGCTAAAATAAAAGTACCCGTCTCTCAGCCCACAGTGAAGA
AAGACAAACGGCAAAATTCTTCAAGGTTTAGCGCAAGCAATAATAGAGAACTTCAAAAACTACCATCCTTAAAAGATGTT
CCTCCTGCTGATCAAAAGAAGTTTTTTATCCAGAAGTTATGTCAGTGTTGCGTCCTTTTTGACTTTGTTTCTGATCCACT
AAGTGAACTAAAGTAGAAGGAATTAAAACGAGCTGCTTTAAGTGAAATGGTAGAATATATCACCCATAATTGGAATGTGA
TCACGGAGCCTATTTACCCAGAAGTAGTCCATATGTTTGCAGTTAACATGTTTCGAATATTACCACCTTCCTCCAATCCT
ACGGGAGCAGAATTTGACCCAGAGGAAGATGAACCAACGTTAGAAGCAGCCTGGCTTCATCTACACTTATTTATGAATTT
TTCTTAAGATTTTTAGAGTCTGCAGATTTCCAATCTAATATAGCGAAGAAATATATTGATCAGAAGTTTGTATTGCAGCT
TTTAAAGCTCTTTGACAGTGAAGATCCTCGGGAGAGAGATTTTCTTAAAACCACCCCTCACAGAATCCATGGGAAATTCC
TAGGCTTGAGAGCTTACATCTGAAAACAGATAAATAATATATTTTATAGGTTTATTTATGAAACAGAGCATCATAATGGC
ATAGCAGAGTTACTGGAAATATTGGGAAGTATAATTAATGGATTTGCCTTACCACTAAAAGAAGAACACAAGATTTTCTT
ATTGAAGGTGCTACTACCTTTGCACAAAGTGAAATCTCTTGAGTGTCTACCACCCCCAGCTGGCATACTGTGGAGTGCAG
TTTTTAGAAAAGGACAGCACCCCCACAGAACCAGTGGTGATGGCACTTCTCAAATGCTGGCCAAAGACTCACAGTCCAAA
AGAAGTAATGTTCTTAAACAAATTAGAAGCGATTTTAGATGTCATTGAACCATCAGAATTTGTGAAGACCATGGAGCCCC
TCTTCCGGCAGTTGGCCAAATGTGTCTCCAGCCCACACTTCCAGGTGACAGAGCGAGCTCTCTATTACTGGAATAATGAA
TACATCATGAGTTTAATCAGTGACAGTGCAGCGAAGATTCTGCCCGTCATGTTTCCTTCCTTGTACCGCAACTCAAAGAC
CCATTGGAACAAGATAATACATGGCTTGATATACAACGCCCTGAAGCTGTTCATAGAGATTAAACAAAAGCTGTTTGATG
ACTGTACACAACAGTCCAAAGCAGAGAAACTAAAAGAGAAGCTAAAAATGGAAGTACGGGAAGAAGCATGGGTTAAAATA
GAAAATCTAGCCAAAGCCAATCCCCAGGTACTAAAA

Alignment

ORF - retro_ggor_1850 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.11 %
• Parental protein coverage: 92.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QESPKAGKSGKSSKEGQDTVESEQISVRKNSLVAVPSTVSAKIKVPVSQPIVKKDKRQNSSRFSASNNRE
          .ESPKAGKSGKSSKEGQDTVESEQISVRKNSLVAVPSTVSAKIKVPVSQP.VKKDKRQNSSRFSASNNRE
Retrocopy KESPKAGKSGKSSKEGQDTVESEQISVRKNSLVAVPSTVSAKIKVPVSQPTVKKDKRQNSSRFSASNNRE

Parental  LQKLPSLKDVPPADQEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITEPIYP
          LQKLPSLKDVPPADQ.K.FIQKL.QCCVLFDFVSDPLS.LK.KE.KRAALSEMVEYITHN.NVITEPIYP
Retrocopy LQKLPSLKDVPPADQKKFFIQKLCQCCVLFDFVSDPLSELK*KELKRAALSEMVEYITHNWNVITEPIYP

Parental  EVVHMFAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQL-VYEFFLRFLESPDFQPNIAKKYIDQK
          EVVHMFAVNMFR.LPPSSNPTGAEFDPEEDEPTLEAAW.HL.L..YEFFLRFLES.DFQ.NIAKKYIDQK
Retrocopy EVVHMFAVNMFRILPPSSNPTGAEFDPEEDEPTLEAAWLHLHL<IYEFFLRFLESADFQSNIAKKYIDQK

Parental  FVLQLLELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSII
          FVLQLL.LFDSEDPRERDFLKTT.HRI.GKFLGLRAYI.KQINNIFYRFIYETEHHNGIAELLEILGSII
Retrocopy FVLQLLKLFDSEDPRERDFLKTTPHRIHGKFLGLRAYI*KQINNIFYRFIYETEHHNGIAELLEILGSII

Parental  NGFALPLKEEHKIFLLKVLLPLHKVKSL-SVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKE
          NGFALPLKEEHKIFLLKVLLPLHKVKSL.SVYHPQLAYC.VQFLEKDST.TEPVVMALLK.WPKTHSPKE
Retrocopy NGFALPLKEEHKIFLLKVLLPLHKVKSL>SVYHPQLAYCGVQFLEKDSTPTEPVVMALLKCWPKTHSPKE

Parental  VMFLNELEEILDVIEPSEFVKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMF
          VMFLN.LE.ILDVIEPSEFVK.MEPLFRQLAKCVSSPHFQV.ERALYYWNNEYIMSLISD.AAKILP.MF
Retrocopy VMFLNKLEAILDVIEPSEFVKTMEPLFRQLAKCVSSPHFQVTERALYYWNNEYIMSLISDSAAKILPVMF

Parental  PSLYRNSKTHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQFKAEKLKEKLKMKEREEAWVKIENLAKANP
          PSLYRNSKTHWNK.IHGLIYNALKLF.E..QKLFDDCTQQ.KAEKLKEKLKM..REEAWVKIENLAKANP
Retrocopy PSLYRNSKTHWNKIIHGLIYNALKLFIEIKQKLFDDCTQQSKAEKLKEKLKMEVREEAWVKIENLAKANP

Parental  QAQK
          Q..K
Retrocopy QVLK

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	2.06 RPM	53.37 RPM
SRP007412_cerebellum	0.95 RPM	25.33 RPM
SRP007412_heart	0.66 RPM	11.54 RPM
SRP007412_kidney	0.65 RPM	26.95 RPM
SRP007412_liver	0.42 RPM	20.65 RPM
SRP007412_testis	1.45 RPM	106.19 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_1850 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1850 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2649
Pan troglodytes	retro_ptro_1784
Pongo abelii	retro_pabe_2322

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000010878	2 retrocopies	retro_ggor_1850 , retro_ggor_7,
Otolemur garnettii	ENSOGAG00000006274	1 retrocopy	retro_ogar_1944,