RetrogeneDB ID: retro_ptro_2164

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 5:75409847..75411562(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INTS6
• Ensembl ID: ENSPTRG00000005890
• Aliases: None
• Description: integrator complex subunit 6 [Source:HGNC Symbol;Acc:14879]

Sequence

>retro_ptro_2164
GAACCAATGGTTATTGATAAACTTCCTCTTGACAAATACGAGTTGGAACCTTCATCACTGACTCAATTTATCCTGGAAAG
GAAATCTCCTGAAACATGTTGGCAGGTGTACGTCAGCAATAGTGCAAAATACAGTGAACTTGGTCATCCTTTTGGTTACT
TGAAAGCCAGTATGGCACTGAACTGTGTCAATTTATTTGTGATGCCTTACAATTACCCAGTCCTTCCCCTCTTAGATGAC
TTGTTTAAAGTGCATAAAGCAAAACCAACATTGAAGTGGAGACAGTCATTTGAAAGTTATTTGAAGACCGTGCCTCCCTA
CTATCTCCGGCCCTTGAAGAAAGCTGTTAGTATGATGGGAGCACCTAACCTAATAGCAGACAGTATGGAATATGGACTTA
GTTACAGTGTCATTTCATACCTCAAAAAACTGAGTCAACAGGCCAAAATAGAATCTGATCGAGTCATTGGATCTGTAGGC
AAGAAAGGAGTACAGGAAACTGGAATAAAAGTCTGGAGCCAATCACATGGTTTATCAAGGGCATATAGGAAAGATTTTCC
ACGACTCCTCCAGGGAATTTCAGAAGACGTCCCTCACAGACTGCTAGACCTTAATATGAAGGAATACGCTGGGTTCCACA
TTGCTTTGCTGAATAAGGATTTGAAGCCACAGACATTTAGAAATGCTTATGACATTCCAAGACGAAATCTTTTGGATCAC
TTAACAAGAATGAGATCTAATCTTTTGAAGCACACTCGCAGATTTCTTAAAGGGCAGGACGAAGATCAAGTGCAGTGTTC
CTATAGCACAAATGGGGAACTACCAGGAATACCTCAAGCAAGTTACCTTCTCCACTAAGAGAACTTGATCCTGATCAGCC
GCAAAGGTTACATACATTTGGCAACTCCTTTAAGCTGGATAAAAAGGGTATGATGACAGATGAAGCAGATGAATTTGTGG
CTGGACCTCAAAATAAACATAAACGACCTGGAGAATCAAATATGCAAGGGGTCCCTAAAAGACGTCAGTGTATGTCTCCA
CTACTAAGAGGCAGACAGCAGAATCCTGTTGTAAACAATCATATCGGGGGAAAAGGACCACCTGCACCTACAACTCAAGC
ACAGCCAGATCTTATTAAGCTTCTTCCTCTTCATAAAATTTCAGAAACCACTAATGATTTGATAATACATGATGTGGTTG
AAAATCATGTTGCAGACCAACTTTCATCAGACATTACACCAAATGCTGTGGATACTGAATTTTCAACATCTTCTCCAGCC
AGTTTACTGGAAGGGCCAACCAATCATATGGAGGCTCCTGGTCATGACAATTTAGGAACCAATGACCTCACTGTTGGTGG
ATTTTTAGAAAATCATGAGGAGCCAAGAGATAAAGAACAATGTGCTGAAGAGAACATACCAGCATCTTCACTCAACACAG
GAAAGAAATTGATCCATTGCAGAAGCCATGAAGAGGTCAATACCGAGCTAAAACCACAAATAATGAAAGAGATCCGAAAG
CCAGGGAGAAAATATGAAAGAATCTTCACTTTACTGAAGCATGTGCAAGGCAGTTTACAAACAAGACTAATATTTTTACA
AAATTTCATTAAAGAAGCATCAAGGTTTTAAAAACGAATGCTAATAGAACAACTGGAGAACTTCTTGGATGAAATTCATC
AAAGAGCCAATCAGATCAACCATATTAATAGCAAT

Alignment

ORF - retro_ptro_2164 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.13 %
• Parental protein coverage: 64.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPMVIDKLPFDKYELEPSPLTQFILERKSPQTCWQVYVSNSAKYSELGHPFGYLKASTALNCVNLFVMPY
          EPMVIDKLP.DKYELEPS.LTQFILERKSP.TCWQVYVSNSAKYSELGHPFGYLKAS.ALNCVNLFVMPY
Retrocopy EPMVIDKLPLDKYELEPSSLTQFILERKSPETCWQVYVSNSAKYSELGHPFGYLKASMALNCVNLFVMPY

Parental  NYPVLLPLLDDLFKVHKAKPTLKWRQSFESYLKTMPPYYLGPLKKAVRMMGAPNLIADSMEYGLSYSVIS
          NYPVL.PLLDDLFKVHKAKPTLKWRQSFESYLKT.PPYYL.PLKKAV.MMGAPNLIADSMEYGLSYSVIS
Retrocopy NYPVL-PLLDDLFKVHKAKPTLKWRQSFESYLKTVPPYYLRPLKKAVSMMGAPNLIADSMEYGLSYSVIS

Parental  YLKKLSQQAKIESDRVIGSVGKKVVQETGIKVRSRSHGLSMAYRKDFQQLLQGISEDVPHRLLDLNMKEY
          YLKKLSQQAKIESDRVIGSVGKK.VQETGIKV.S.SHGLS.AYRKDF..LLQGISEDVPHRLLDLNMKEY
Retrocopy YLKKLSQQAKIESDRVIGSVGKKGVQETGIKVWSQSHGLSRAYRKDFPRLLQGISEDVPHRLLDLNMKEY

Parental  TGFQVALLNKDLKQRTFXXAYDIPRRNLLDHLTRMRSNLLKSTRRFL-KGQDEDQVHSVPIAQMGNYQEY
          .GF..ALLNKDLK..TF..AYDIPRRNLLDHLTRMRSNLLK.TRRFL.KG.......SVPIAQMGNYQEY
Retrocopy AGFHIALLNKDLKPQTFRNAYDIPRRNLLDHLTRMRSNLLKHTRRFL>KGRTKIKC-SVPIAQMGNYQEY

Parental  LKQV-PSPLRELDPDQPRRLHTFGNPFKLDKKGMMIDEADEFVAGPQNKHKRPGEPNMQGIPKRRRCMSP
          LKQV.PSPLRELDPDQP.RLHTFGN.FKLDKKGMM.DEADEFVAGPQNKHKRPGE.NMQG.PKRR.CMSP
Retrocopy LKQV>PSPLRELDPDQPQRLHTFGNSFKLDKKGMMTDEADEFVAGPQNKHKRPGESNMQGVPKRRQCMSP

Parental  LLRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIKPLPLHKISETTNDSIIHDVVENHVADQLSSDITPNAM
          LLRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIK.LPLHKISETTND.IIHDVVENHVADQLSSDITPNA.
Retrocopy LLRGRQQNPVVNNHIGGKGPPAPTTQAQPDLIKLLPLHKISETTNDLIIHDVVENHVADQLSSDITPNAV

Parental  DTEFSASSPASLLERPTNHTEALGHDHLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNKGKKLMHC
          DTEFS.SSPASLLE.PTNH.EA.GHD.LGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLN.GKKL.HC
Retrocopy DTEFSTSSPASLLEGPTNHMEAPGHDNLGTNDLTVGGFLENHEEPRDKEQCAEENIPASSLNTGKKLIHC

Parental  RSHEEVNTELKAQIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQNVIKEASRFKKRMLIEQLENFLD
          RSHEEVNTELK.QIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQN.IKEASRF.KRMLIEQLENFLD
Retrocopy RSHEEVNTELKPQIMKEIRKPGRKYERIFTLLKHVQGSLQTRLIFLQNFIKEASRF*KRMLIEQLENFLD

Parental  EIHRRANQINHINSN
          EIH.RANQINHINSN
Retrocopy EIHQRANQINHINSN

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	0.21 RPM	10.92 RPM
SRP007412_cerebellum	0.36 RPM	15.70 RPM
SRP007412_heart	0.44 RPM	14.31 RPM
SRP007412_kidney	0.44 RPM	16.63 RPM
SRP007412_liver	0.33 RPM	11.98 RPM
SRP007412_testis	7.38 RPM	150.80 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2164 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2164 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2164 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3307
Gorilla gorilla	retro_ggor_1307
Pongo abelii	retro_pabe_2727

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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,
Pan troglodytes	ENSPTRG00000005890	1 retrocopy	retro_ptro_2164 ,
Pan troglodytes	ENSPTRG00000041730	1 retrocopy	retro_ptro_2285,