RetrogeneDB ID: retro_ggor_1307

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 17:53950292..53952001(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INTS6
• Ensembl ID: ENSGGOG00000001176
• Aliases: None
• Description: None

Sequence

>retro_ggor_1307
CCAATGGTTATTGATAAACTTCCTTTTGACAAATACGAGTTGGAACCTTCATCACTGACTCAATTTATCCTGGAAAGGAA
ATCTCAAACATGTTGGCAGGTGTACGTCAGCAATAGTTCAAAATACAGTGAACTTGGTCATCCTTTTGGTTACTTGAAAG
CCAGTATGGCACTGAACTGTGTCAATTTATTTGTGATGCCTTACAATTACCCAGTCCTTCCCCTCTTAGATGACTTGTTT
AAAGTGCATAAAGCAAAACCAACATTGAAGTGGAGACAGTCATTTGAAAGTTATTTGAAGACCGTGCCTCCCTACTATCT
CGGGCCCTTGAAGAAAGCTGTTAGTATGATGGGAGCACCTAACCTAATAGCAGACAGTATGGAATATGGACTTAGTTACA
GTGTCATTTCATACCTCAAAAAACTGAGTCAACAGGCCAAAATAGAATCTGATCGAGTCATTGGATCTGTAGGCAAAAAA
GGAGTATAGGAAACTGGAATAAAAGTCTGGAGCCAATCACATGGTTTATCAAGGGCATATAGGAAAGATTTTCCACGACT
CCTCCAGGGAATTTCAGAAGATGTCCCTCACAGACTGCTAGACCTTAATATGAAGGAATACCCTGGGTTCCATATTGCTT
TGCTGAATAAGGATTTGAAGCCACAGACATTTAGAAATGCTTATGACATTCCAAGATGAAATCTTTTGGATCACTTAACA
AGAATGAGATCTAATCTTTTGAAGCACACTCGCAGATTTCTTAAAGGACAGGACGAAGATCAAGTGCAGTGTTCCTATAG
CACAAATGGGGAACTACCAGGAATACCTCAAGCAAGTTACCTTCTCCACTAAGAGAACTTGATCCTGATCAGCCGCAAAG
GTTACATACATTTGGCAACTCCTTTAAGCTGGATAAAAAGGGTATGATGACAGATGAAGCAGATGAATTTGTGGCTGGAC
CTCAAAATAAATATAAACGACCTGGAGAATCAAATATGCAAGGGATCCCTAAAAGACGTCAGTGTATGTCTCCACTACTA
AGAGGCAGACAGCAGAATCCTGTTGTAAACAATCATATCGGGGGAAAAGGACCACCTGCACCTACAACTCAAGCACAGCC
AGATCTTATTAAGCTTCTTCCTCTTCATAAAATTTCAGAAACCACTAATGATTCGATAATACATGATGTGGTTGAAAATC
ATGTTGCAGACCAACTTTCATCAGACATTACACCAAATGCTATGGATATTGAATTTTCAACATCTTCTCCAGGCAGTTTA
CTGGAAACGCCAACCAATCATATGGAGGCTCCTGGTCATGACAATTTAGGAACCAATGACCTCACTGTTGGTGGATTTTT
AGAAAATCACGAGGAGCCAAGAGATAAAGAACAATGTGCTGAAGAGAACATACCAGCATCTTCACTCAACACAGGAAAGA
AATTGATCCATTGCAGAAGCCATGAAGAGGTCAATACCAAGCTAAAACCACAAATAATGAAAGAGATCCGAAAGCCAGGG
AGAAAATATGAAAGAATCTTCACTTTACTGAAGCATGTGCAAGGCAGTTTACAAACAAGACTAATATTTTTACAAAATGT
CATTAAAGAAGCATCAAGGTTTTAAAAACGAATGCTAATAGAACAACTGGAGAACTTCTTGGATGAAATTCATCGAAGAG
CCAATCAGATCAACCATATTAATAGCAAT

Alignment

ORF - retro_ggor_1307 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.46 %
• Parental protein coverage: 64.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PMVIDKLPFDKYELEPSPLTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKASTALNCVNLFVMPYN
          PMVIDKLPFDKYELEPS.LTQFILERKS.QTCWQVYVSNS.KYSELGHPFGYLKAS.ALNCVNLFVMPYN
Retrocopy PMVIDKLPFDKYELEPSSLTQFILERKS-QTCWQVYVSNSSKYSELGHPFGYLKASMALNCVNLFVMPYN

Parental  YPVLLPLLDDLFKVHKAKPTLKWRQSFESYLKTMPPYYLGPLKKAVRMMGAPNLIADSMEYGLSYSVISY
          YPVL.PLLDDLFKVHKAKPTLKWRQSFESYLKT.PPYYLGPLKKAV.MMGAPNLIADSMEYGLSYSVISY
Retrocopy YPVL-PLLDDLFKVHKAKPTLKWRQSFESYLKTVPPYYLGPLKKAVSMMGAPNLIADSMEYGLSYSVISY

Parental  LKKLSQQAKIESDRVIGSVGKKVVQETGIKVRSRSHGLSMAYRKDFQQLLQGISEDVPHRLLDLNMKEYT
          LKKLSQQAKIESDRVIGSVGKK.V.ETGIKV.S.SHGLS.AYRKDF..LLQGISEDVPHRLLDLNMKEY.
Retrocopy LKKLSQQAKIESDRVIGSVGKKGV*ETGIKVWSQSHGLSRAYRKDFPRLLQGISEDVPHRLLDLNMKEYP

Parental  GFQVALLNKDLKPQTFRNAYDIPRRNLLDHLTRMRSNLLKSTRR-FLKGQDEDQVHSVPIAQMGNYQEYL
          GF..ALLNKDLKPQTFRNAYDIPR.NLLDHLTRMRSNLLK.TRR.FLK........SVPIAQMGNYQEYL
Retrocopy GFHIALLNKDLKPQTFRNAYDIPR*NLLDHLTRMRSNLLKHTRR>FLKDRTKIKC-SVPIAQMGNYQEYL

Parental  KQV-PSPLRELDPDQPRRLHTFGNPFKLDKKGMMIDEADEFVAGPQNKHKRPGEPNMQGIPKRRRCMSPL
          KQV.PSPLRELDPDQP.RLHTFGN.FKLDKKGMM.DEADEFVAGPQNK.KRPGE.NMQGIPKRR.CMSPL
Retrocopy KQV>PSPLRELDPDQPQRLHTFGNSFKLDKKGMMTDEADEFVAGPQNKYKRPGESNMQGIPKRRQCMSPL

Parental  LRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIKPLPLHKISETTNDSIIHDVVENHVADQLSSDITPNAMD
          LRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIK.LPLHKISETTNDSIIHDVVENHVADQLSSDITPNAMD
Retrocopy LRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIKLLPLHKISETTNDSIIHDVVENHVADQLSSDITPNAMD

Parental  TEFSASSPAGLLERPTNHTEALGHDHLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKLMHCR
          .EFS.SSP..LLE.PTNH.EA.GHD.LGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLN.GKKL.HCR
Retrocopy IEFSTSSPGSLLETPTNHMEAPGHDNLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNTGKKLIHCR

Parental  SHEEVNTELKAQIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRFKKRMLIEQLENFLDE
          SHEEVNT.LK.QIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRF.KRMLIEQLENFLDE
Retrocopy SHEEVNTKLKPQIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRF*KRMLIEQLENFLDE

Parental  IHRRANQINHINSN
          IHRRANQINHINSN
Retrocopy IHRRANQINHINSN

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	13.52 RPM
SRP007412_cerebellum	0.00 RPM	13.71 RPM
SRP007412_heart	0.00 RPM	4.28 RPM
SRP007412_kidney	0.00 RPM	19.83 RPM
SRP007412_liver	0.00 RPM	19.70 RPM
SRP007412_testis	0.52 RPM	203.47 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_1307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_1307 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3307
Pan troglodytes	retro_ptro_2164
Pongo abelii	retro_pabe_2727

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000102786	1 retrocopy	retro_hsap_3307,
Gorilla gorilla	ENSGGOG00000001176	1 retrocopy	retro_ggor_1307 ,
Pongo abelii	ENSPPYG00000005381	1 retrocopy	retro_pabe_2727,
Pan troglodytes	ENSPTRG00000005890	1 retrocopy	retro_ptro_2164,