RetrogeneDB ID: retro_pabe_2727

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:40686680..40688399(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INTS6
• Ensembl ID: ENSPPYG00000005381
• Aliases: None
• Description: integrator complex subunit 6 [Source:HGNC Symbol;Acc:14879]

Sequence

>retro_pabe_2727
GAACCAATGGTTATTGATAAACTTCCTTTTGACAAATACGAGTAGGAACCTTCATCACTGACTCAATTTATCCTGGAAAG
GAAATCTCCTCAAACATGTTGGCAGGTATACGTCAGCAATAGTGCAAAATATAGTGAACTTGGTCATCCTTTTGGTTACT
TGAAAGCCAGTACAGCACTGAACTGTGTCAATTTATTTGTGATGCCTTAATAATTATCCAGTCCTTCTTCCCCTCTTAGA
TGACTTGTTTAAAATGCATAAAGCAAAACCAACCTTGAAGTGGAGACAGCCATTTGAAAGTTATTTGAAGACCATGCCTC
CCTACTATCTCGGGCCCTTGAAGAAAGCTGTTAGTATGATGGGAGCACCTAACCTAATAGCAGACGGTATGGAATATGGA
CTTAGTTACAGTGTCATTTCATACCTCAAAAAACTGAGTCAACAGGCCAAAATAGAATCTGATCGAGTCATTGGATCTGT
AGGTAAAAAAGGAGTACAGGTAACTGGAATAAAAGTCTGGAGCCGATCACATGGTTTATCAAGGGCATATAGGAAAGATT
TTCAACAACTTCTCCAGGGAATTTCAGACGATGTCCCTCACAGACTGCTAGACCTTAATATGAAGGAATACACTGGGTTC
CAAGTTGCTTTGCTGAATAAGGATTTGAAGCCACAGACATTTAGAAATGCTTATGACATAACAAGACGAAATCTTTTGGA
TCACTTAACAAGAATGAGATCTAATCTTTTGAAGCACACTCGCAGATTTCTTAAAGGACAGGACAAAGATCAAGTGCACA
GTGTTCCTATAGCACAAATGGGGAACTACCAGGAATACCTCAAGCAAGTACCTTCTCCACTAAGAGAACTTGATCCTGAT
CAGCCGCGAAGGTTGCATACATTTGGCAACTCCTTTAAGCTGGATAAGAAGGGTATGATGACAGATGAAGCAGATGAATT
TGTGGCTAGACCTCAAAATAAACATAAACGACCTGGAGAATCAAATATGCAAGGGATCCCTAAAAGACGTCAGTGTATGT
CTCCACTACTAAGAGGCAGACAGCAGAATCCTGTTATAAACAATCATATCGGGGGAAAAGGACCACCTGCATGTACAACT
CAAGCACAGCCAGATCTTATTAAGCTTCTTCCTCTTCATAAAATTTCAGAAACCACTAATGATTCGATAATACATGATGC
GGTTGAAAATCATGTTGCAGACCAACTTTCATCAGACACTACACCAAATGCTATGGATACTGAATTTTCAACATCTTCTC
CAGCCAGTTTACTGGAACGGCCAACCAATCACATGGAGGCTCTTGGTCATGACCATTTAGGAACCAATGACCTCACTGTT
GGTGGATTTTTAGAAAATCATGAGGAGCCAAGAGATAAAGAACAATGTGCTGAAGAGAACATACCAGCATCTTCACTCAA
CAAAGGAAAGAAATTGATGCATTGCAGAAGCCATGAAGAGGTCAATACCGAACTAAAACCACAAATAATGAAAGAGATAG
GAAAGCCAGGGAGAAAATATGAAAGAATCTTCACTTTACTGAAGCATGTGCAAGGCAGTTTACAAACAAGACTAATATTT
TTACAAAATGTCATTAAAGAAGCATCAAAGTTTTAAAAACGAATGCTAATAGAACAACTGGAGAACTTCTTAGATGAATT
CATCTAAGAGCCAATCAGATCAACCATATTAATAGCAAT

Alignment

ORF - retro_pabe_2727 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.91 %
• Parental protein coverage: 64.6 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPMVIDKLPFDKYELEPSPLTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKASTALNCVNLFVMP-
          EPMVIDKLPFDKYE.EPS.LTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKASTALNCVNLFVMP.
Retrocopy EPMVIDKLPFDKYE*EPSSLTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKASTALNCVNLFVMP>

Parental  YNYPVLLPLLDDLFKVHKAKPTLKWRQSFESYLKTMPPYYLGPLKKAVRMMGAPNLIADSMEYGLSYSVI
          .NYPVLLPLLDDLFK.HKAKPTLKWRQ.FESYLKTMPPYYLGPLKKAV.MMGAPNLIAD.MEYGLSYSVI
Retrocopy NNYPVLLPLLDDLFKMHKAKPTLKWRQPFESYLKTMPPYYLGPLKKAVSMMGAPNLIADGMEYGLSYSVI

Parental  SYLKKLSQQAKIESDRVIGSVGKKVVQETGIKVRSRSHGLSMAYRKDFQQLLQGISEDVPHRLLDLNMKE
          SYLKKLSQQAKIESDRVIGSVGKK.VQ.TGIKV.SRSHGLS.AYRKDFQQLLQGIS.DVPHRLLDLNMKE
Retrocopy SYLKKLSQQAKIESDRVIGSVGKKGVQVTGIKVWSRSHGLSRAYRKDFQQLLQGISDDVPHRLLDLNMKE

Parental  YTGFQVALLNKDLKPQTFRNAYDIPRRNLLDHLTRMRSNLLKSTRRFLKGQDEDQVHSVPIAQMGNYQEY
          YTGFQVALLNKDLKPQTFRNAYDI.RRNLLDHLTRMRSNLLK.TRRFLKGQD.DQVHSVPIAQMGNYQEY
Retrocopy YTGFQVALLNKDLKPQTFRNAYDITRRNLLDHLTRMRSNLLKHTRRFLKGQDKDQVHSVPIAQMGNYQEY

Parental  LKQVPSPLRELDPDQPRRLHTFGNPFKLDKKGMMIDEADEFVAGPQNKHKRPGEPNMQGIPKRRRCMSPL
          LKQVPSPLRELDPDQPRRLHTFGN.FKLDKKGMM.DEADEFVA.PQNKHKRPGE.NMQGIPKRR.CMSPL
Retrocopy LKQVPSPLRELDPDQPRRLHTFGNSFKLDKKGMMTDEADEFVARPQNKHKRPGESNMQGIPKRRQCMSPL

Parental  LRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIKPLPLHKISETTNDSMIHDVIENHVADQLSSDITPNAMD
          LRGRQQNPV.NNHIGGKGPPA.TTQAQPDLIK.LPLHKISETTNDS.IHD..ENHVADQLSSD.TPNAMD
Retrocopy LRGRQQNPVINNHIGGKGPPACTTQAQPDLIKLLPLHKISETTNDSIIHDAVENHVADQLSSDTTPNAMD

Parental  TEFSTSSPASLLERPTNHTEALGHDHLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKLMHCR
          TEFSTSSPASLLERPTNH.EALGHDHLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKLMHCR
Retrocopy TEFSTSSPASLLERPTNHMEALGHDHLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKLMHCR

Parental  SHEEVNTELKAQIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRFKKRMLIEQLENFLDE
          SHEEVNTELK.QIMKEI.KPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEAS.F.KRMLIEQLENFLDE
Retrocopy SHEEVNTELKPQIMKEIGKPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASKF*KRMLIEQLENFLDE

Parental  -IHRRANQINHINSN
          .IH.RANQINHINSN
Retrocopy <IHLRANQINHINSN

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	0.06 RPM	11.28 RPM
SRP007412_cerebellum	0.12 RPM	18.85 RPM
SRP007412_heart	0.06 RPM	15.44 RPM
SRP007412_kidney	0.13 RPM	15.51 RPM
SRP007412_liver	0.09 RPM	20.04 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2727 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2727 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2727 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3307
Pan troglodytes	retro_ptro_2164
Gorilla gorilla	retro_ggor_1307

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 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 ,
Pongo abelii	ENSPPYG00000020755	1 retrocopy	retro_pabe_2766,
Pan troglodytes	ENSPTRG00000005890	1 retrocopy	retro_ptro_2164,