RetrogeneDB ID: retro_ggor_3044

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: X:90268484..90270477(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP2B1
• Ensembl ID: ENSGGOG00000015593
• Aliases: None
• Description: None

Sequence

>retro_ggor_3044
ATGACTGACTCCAAGTATTTCACAACCAATAAAAAAGCAGAAATATTTGAACTAAAAGCTGAACTCAATAATGAAAAGAA
AGAAAAGAGAAAGGAGGCTGTGAAGAAAGTGATTGCTGTTATTACCGTGGGGAAGGATGTTAGTTCTGTCTTTCCAGACA
TAGTGAACTGTATGCAGACTGACAATCTGAAACTAAAGAAGCTTGTGTATCTCTACTTGATGAACTATGCCAAGAGTCAG
CCAGACATGGCCATCATAGCTGTAAATAGCTTTGTGAAGGACTGTGAAGATCCTAATCTTTTGATTCAAGCCTTGGCAGT
CAGAACCATGGGGTGCATCTGGGTAGACAAAATTACAGAATATCTCTCTGAGCCCCTTCTCAAGTGCTTAGAGGATGAGG
ATCCCTATGTTCGGAAAACAGCAGCAGTATGCGTGGCAAAACTCCATGATATCAACGCCCAAATGGTGGAAGATCAGGGA
TTTTTGGATTATCTATGGGGTCTCATAGCAGATTCAAATCCAATGGTGGTGGCTAATGCTGTAGCAGCATTATCTGAAAT
CAGTGAGTCTCACCCAAACAGCAACTTACTCAATCTGAACACACAGAACATTAATAAGCTGCGGACAGCCCTGAATAAGT
GCACTGAAGGGGCCAGATTTTCATGCTGGACTGCCTGTCTAATTACAACCCTAAAAATGATCGGAAGGCTCAGAGCATCT
GTGAGCGGGTAACTCCCCAGCTATCCCATGCCAACTCAGCAGTGGTGCTTTCAGTGGTAAAAGTACTAATGAAGTTTCTA
GAATTGTTACCTAAGGATTCTGACTACTATAATATGCTGCTGAAGAAGTTAGCCCCTCCACTTGTCACTTTGATGTCTGG
GGAGTCAGAAGTGCAGTATGTCTCCCTGAGAAACATCAACTTAATTGTCCAGAAAAGGCCTGAAATCTTGAAGCAGGAAA
TCAAAGTCTTCTTTGTGAAGTACAATGATCCCATCTATGTTAAACTAGAGAAGTTGGACATCAGGATTTATTTGGCATCA
CAAGCCAACATTGCTCAGGTTCTGGCAGAACTGAAGGAATATGCCACAGAGGTGAATGTTGACTTTGTTCGAAAAGCTGT
GTGGGCCACTGGACGGTGTGCCATCAAGGTGGAGCAATCTGCAGAGCACTGTGTAAGCACATTGCTTGATCTAATCAAGA
CCAAAGTGAATTATGTGGTCCAAGAAGTGATTGCTGTCATCAGGGACATCTTCCGCAAATACTCCAACAAGTATGAAAGT
ATCATTGCCACTCTATGTGAGAACTTAGACTCGCTGGATGAGCCAGATGCTCGATCGGCTATGATTTGGATTGTGGGAGA
ATAAGCTGAAAGAATTGACAATGCAGATGAGTTACTAGAAAGCTTCCTGGAGGGTTTTCATGATGAAAACACCCAGGAGC
AGCTCACTCTGCTTACTGCCATAATGAAGCTGTTTCTCAAGAAACCACCAAAACACAAGAGCTAGTCCAGCAGATGTTGA
CTTTGGCAACACAGGATTCTGATAATCCTGACCTTCGAGAACGGGGCTATACTTATTGGGCTCTTCTCTCAGCTGACCCT
GTCACGGCTAAAGAAGTAGTCTTGTCTGAGAAGCCACTGATCTCTCAGGAGACGGAACTTATTGAGCCAACTGCGTTGGA
GGAGCTAATCTGCCACATTGGTTCTTTGGCCTCTGTGTATCATAAGCCTTCCAATGCTTTTGTGGAAGGAAGTCATGGAA
TCCATCGTAAACACTTGCCAATTCATCATGGGAGCACTGATGCAGGTGACAGCCCTGTTGGCACCACCACCGCAACGAAC
CTGGAACAGCCCCAGGTTATACCCTCTCAAGGTGATCTTCTGGGGAGTCTTTTAAACCTTGACCTCAGTCTCCCAATCAA
TGTGCCACAGGTGTCCTCCATGCAGATGGGAGCAGTGGATCTCCTAGGAGGAGGACTAGATAGTCTGGTGGGA

Alignment

ORF - retro_ggor_3044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.4 %
• Parental protein coverage: 73.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTDSKYFTTNKKGEIFELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVNCMQTDNLELKKLVY
          MTDSKYFTTNKK.EIFELKAELNNEKKEKRKEAVKKVIA..TVGKDVSS.FPD.VNCMQTDNL.LKKLVY
Retrocopy MTDSKYFTTNKKAEIFELKAELNNEKKEKRKEAVKKVIAVITVGKDVSSVFPDIVNCMQTDNLKLKKLVY

Parental  LYLMNYAKSQPDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKT
          LYLMNYAKSQPDMAI.AVNSFVKDCEDPN.LI.ALAVRTMGCI.VDKITEYL.EPL.KCL.DEDPYVRKT
Retrocopy LYLMNYAKSQPDMAIIAVNSFVKDCEDPNLLIQALAVRTMGCIWVDKITEYLSEPLLKCLEDEDPYVRKT

Parental  AAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISESHPNSNLLDLNPQNINKLLTA
          AAVCVAKLHDINAQMVEDQGFLD.L..LIADSNPMVVANAVAALSEISESHPNSNLL.LN.QNINKL.TA
Retrocopy AAVCVAKLHDINAQMVEDQGFLDYLWGLIADSNPMVVANAVAALSEISESHPNSNLLNLNTQNINKLRTA

Parental  LNECTEW-GQIFILDCLSNYNPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFLELLPKDSDYYNM
          LN.CTE..GQIF.LDCLSNYNPK.DR.AQSICERVTP.LSHANSAVVLS.VKVLMKFLELLPKDSDYYNM
Retrocopy LNKCTEG<GQIFMLDCLSNYNPKNDRKAQSICERVTPQLSHANSAVVLSVVKVLMKFLELLPKDSDYYNM

Parental  LLKKLAPPLVTLLSGEPEVQYVALRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIMIRLASQA
          LLKKLAPPLVTL.SGE.EVQYV.LRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDI.I.LASQA
Retrocopy LLKKLAPPLVTLMSGESEVQYVSLRNINLIVQKRPEILKQEIKVFFVKYNDPIYVKLEKLDIRIYLASQA

Parental  NIAQVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIRDIFR
          NIAQVLAELKEYATEV.VDFVRKAV.A.GRCAIKVEQSAE.CVSTLLDLI.TKVNYVVQE.I.VIRDIFR
Retrocopy NIAQVLAELKEYATEVNVDFVRKAVWATGRCAIKVEQSAEHCVSTLLDLIKTKVNYVVQEVIAVIRDIFR

Parental  KYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNADELLESFLEGFHDESTQVQLTLLTAIV
          KY.NKYESIIATLCENLDSLDEPDAR.AMIWIVGE.AERIDNADELLESFLEGFHDE.TQ.QLTLLTAI.
Retrocopy KYSNKYESIIATLCENLDSLDEPDARSAMIWIVGE*AERIDNADELLESFLEGFHDENTQEQLTLLTAIM

Parental  KLFLKKP-SETQELVQQVLSLATQDSDNPDLRDRGYIYWRLLSTDPVTAKEVVLSEKPLISEETDLIEPT
          KLFLKKP...TQELVQQ.L.LATQDSDNPDLR.RGY.YW.LLS.DPVTAKEVVLSEKPLIS.ET.LIEPT
Retrocopy KLFLKKP<TKTQELVQQMLTLATQDSDNPDLRERGYTYWALLSADPVTAKEVVLSEKPLISQETELIEPT

Parental  LLDELICHIGSLASVYHKPPNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL
          .L.ELICHIGSLASVYHKP.NAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL
Retrocopy ALEELICHIGSLASVYHKPSNAFVEGSHGIHRKHLPIHHGSTDAGDSPVGTTTATNLEQPQVIPSQGDLL

Parental  GDLLNLDLGPPVNVPQVSSMQMGAVDLLGGGLDSLLG
          G.LLNLDL..P.NVPQVSSMQMGAVDLLGGGLDSL.G
Retrocopy GSLLNLDLSLPINVPQVSSMQMGAVDLLGGGLDSLVG

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	0.38 RPM	116.53 RPM
SRP007412_cerebellum	0.24 RPM	57.80 RPM
SRP007412_heart	0.16 RPM	27.61 RPM
SRP007412_kidney	0.86 RPM	71.92 RPM
SRP007412_liver	0.32 RPM	21.42 RPM
SRP007412_testis	6.94 RPM	456.98 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_3044 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_3044 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014853	1 retrocopy	retro_cjac_1850,
Gorilla gorilla	ENSGGOG00000015593	1 retrocopy	retro_ggor_3044 ,
Myotis lucifugus	ENSMLUG00000002837	1 retrocopy	retro_mluc_2443,
Nomascus leucogenys	ENSNLEG00000013939	2 retrocopies	retro_nleu_1925, retro_nleu_2554,