RetrogeneDB ID: retro_ggor_2258

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:53651742..53652813(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL1
• Ensembl ID: ENSGGOG00000008198
• Aliases: None
• Description: None

Sequence

>retro_ggor_2258
AAAAAAGCAGTTCTACAAGGCGAGCCAGCTGGTCAGTGAGAAGGTCGGAGGGGCTGAGGGGACCAAGCTGGACGATGACT
TCAAAGAGATGGAGATGTCATCAGCAAGGCGGTGACGGAAATGCTGGCAAGGACCATCAAGTACCTGCAGCCCAACCCAG
CCTCTCAGGCTAAGCTGACCATGCTCAACACGGTGTGCAAGATCCAGGGCCAGGTGAAGAACCCCAGCTACCCGCAGTCG
GAGGGGCTCCTGAGCGAGTGCCTGATCTGCCACCAGAAGGAGCTGGGCAACAAGTCCAACTTCAGTGACGCACTGCTGGA
TGCCGGCGAGTCCATGAAGCACCTGGCAGAGGTGAAGGACTCCCTGGACATAGAGGTCAAGCAGAACTTCATTGACCTCC
TCCAGAACCTGTGTGAGAAAGACCTGAAGGGGATCCAGCACCACCTGCAGAAGCTAGAGGGCCGCCGCCTGGACTTTGAC
TAAAAGAAGCGGCAGGGCAAGATCCCCGATGAGGAGCTGCGCCAGGCGCTGGAGAAGTTTGAGGACTCCAAGGAGGTAGC
AGAAACCAGCATGCACAACCTCCTGGAGACCGACATTGAGCAGGTGAGTCAACTCCGGGCCCTGGCGGAGGCGCAGCTGA
ACTACCACTGGCAGGCCATGCAGATCCTGGACGAGCTGGCAGAGAAGCTCAAGCGCAGGATGCGGGAAGCTTCCTCACGC
CCCAAGCAGGAGTATAAGCCCAAGTTCCGGGAGCCCTTTGACCTCGGAGAGCCTGAGCAGTCCAACGGGGGCTTCCCCTG
CACCACAGTCCCCAAGATCGCAGCTTCATCCCCTTTCCGATCTTCCGACAAGTCCATCCGGACTCCTAGCAGGAGCATGC
CGCCCCTAGACCAGCCAAGCTGCAAGGTACTGTATGACTTCCAGCCTGAGAACCATGGGGAGCTGGGCTTCCATGAGGGC
GATGTCTTCACGCTGATCAACCAGATCAACGAGAACTGGTACCAGGGCATGCTGGACAGCCAGTTGGGCTTCTTCCTGCT
CAGCTACGTGGACGTGCTCGTGCCTCTGCCC

Alignment

ORF - retro_ggor_2258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.82 %
• Parental protein coverage: 96.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KASQLVSEKVGGAEGTKL--DDDFKEMEKKVDVTSKAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRG
          K...L..E..G..EG.....D..........DV.SKAVTE.LARTI.YLQPNPAS.AKLTMLNTV.KI.G
Retrocopy KKAVLQGEPAGQ*EGRRG*GDQAGR*LQRDGDVISKAVTEMLARTIKYLQPNPASQAKLTMLNTVCKIQG

Parental  QVKNPGYPQSEGLLGECMIRHGKELGGESNFGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEK
          QVKNP.YPQSEGLL.EC.I.H.KELG..SNF.DALLDAGESMK.LAEVKDSLDIEVKQNFID.LQN....
Retrocopy QVKNPSYPQSEGLLSECLICHQKELGNKSNFSDALLDAGESMKHLAEVKDSLDIEVKQNFIDLLQNXXXX

Parental  DLKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALV
          ............EGRRLDFD.KK.RQGKIPDEELRQALEKFE.SKEVAETSMHNLLETDIEQVSQL.AL.
Retrocopy XXXXXXXXXXXXEGRRLDFD*KK-RQGKIPDEELRQALEKFEDSKEVAETSMHNLLETDIEQVSQLRALA

Parental  DAQLDYHRQAVQILDELAEKLKRRMREASSRPKREYKPKPREPLDLGEPEQSNGGFPCTTAPKIAASSSF
          .AQL.YH.QA.QILDELAEKLKRRMREASSRPK.EYKPK.REP.DLGEPEQSNGGFPCTT.PKIAASS.F
Retrocopy EAQLNYHWQAMQILDELAEKLKRRMREASSRPKQEYKPKFREPFDLGEPEQSNGGFPCTTVPKIAASSPF

Parental  RSSDKPIRTPSRSMPPLDQPSCKALYDFEPENDGELGFREGDVITLTNQIDENWYEGMLDGQSGFFPLSY
          RSSDK.IRTPSRSMPPLDQPSCK.LYDF.PEN.GELGF.EGDV.TL.NQI.ENWY.GMLD.Q.GFF.LSY
Retrocopy RSSDKSIRTPSRSMPPLDQPSCKVLYDFQPENHGELGFHEGDVFTLINQINENWYQGMLDSQLGFFLLSY

Parental  VEVLVPLP
          V.VLVPLP
Retrocopy VDVLVPLP

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	0.91 RPM	31.41 RPM
SRP007412_cerebellum	1.97 RPM	36.99 RPM
SRP007412_heart	0.41 RPM	11.54 RPM
SRP007412_kidney	0.57 RPM	19.63 RPM
SRP007412_liver	0.47 RPM	19.36 RPM
SRP007412_testis	1.76 RPM	27.76 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_2258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2258 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1742

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000141985	3 retrocopies	retro_hsap_1742, retro_hsap_1745, retro_hsap_1859,
Gorilla gorilla	ENSGGOG00000008198	3 retrocopies	retro_ggor_2151, retro_ggor_2258 , retro_ggor_675,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Monodelphis domestica	ENSMODG00000000931	1 retrocopy	retro_mdom_1530,
Nomascus leucogenys	ENSNLEG00000003122	2 retrocopies	retro_nleu_2914, retro_nleu_3075,
Pongo abelii	ENSPPYG00000009405	6 retrocopies	retro_pabe_1488, retro_pabe_1516, retro_pabe_1530, retro_pabe_1542, retro_pabe_1700, retro_pabe_3542,