RetrogeneDB ID: retro_ggor_2019

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:25639005..25639843(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ISYNA1
• Ensembl ID: ENSGGOG00000016939
• Aliases: None
• Description: None

Sequence

>retro_ggor_2019
TCTGGGTCCCCACAGAACACTCTGGTGCCCGGAGCCCTTGAGCTCGCGTGGCAGCGCCAGGTTTACGTGGGCGGAGATGA
CTTCAAGTCAGGCCAGACCAAAGTCAAGTCCGTGCTCGTGGACTTCCTCATCGGCTATGGCCTCAAGACCAAGTCGATTG
TGAATTATAACCACCTGGGGAACAACGACCGGCAGAACCTGTTGGCGCCATCGCTGTTCCCTCTGAGGCGGTGTCCAAGA
GCAACGTAGTGGACGACATGGCGCAAAGACACCCAGTGCTCTACGCGCCTGGCGAGGAGCCTGACCGCTGCGCGGTCATC
AAGTACATGCCGTACGCGGGTGACCCCAAGCGTGCGCTGGATGAGTCTACCTTGGAGCTGATGCTGGGCGTAACCAACAC
GCTGGTACTGCACAACACGTGCGAGGACTCGCTGCTGGCCGCCCCCATCATCCTGGACCTGGCGCTGCTGACCGAGCTGT
GCCACTGCGTGAGCTTCTGCACCAATGACAACACCGAGCCACAGACCTTCCACCCCATGCCGTCCCTGCTTAGCATCTCT
TCAAGGTGCCGCCGGGCAGCCCGGTGGTCAGTGCGCTTTTCCGCCAGCTCAGCTGCATCGAGAACATCCACAGGGCCTGT
GTGGGGCTTCCGCCACAGAACCACGTGGTCCTGGTGCACAAGATGGAGCTCCCAGTGCCTGGCCTCAAGTGAGTCGGACC
TGTGGCTGCCGCCTGCCCTGTGTTGAACAAGAAAGGACCGGTACCCGCTGCCACCAATGGCTGTACCAGTGATACCAATG
GACACCCACAGGTGGAGGAACCCCAGATGCACACCACC

Alignment

ORF - retro_ggor_2019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.6 %
• Parental protein coverage: 50.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGSPQNTLVPGALELAWQHRVFVGGDDFKSGQTKVKSVLVDFLIGSGLKTMSIVSYNHLGNNDGENLSAP
          .GSPQNTLVPGALELAWQ..V.VGGDDFKSGQTKVKSVLVDFLIG.GLKT.SIV.YNHLGNND..NL.AP
Retrocopy SGSPQNTLVPGALELAWQRQVYVGGDDFKSGQTKVKSVLVDFLIGYGLKTKSIVNYNHLGNNDRQNLLAP

Parental  LQFR-SKEVSKSNVVDDMVQSNPVLYTPGEEPDHCVVIKYVPYVGDSKRALDEYTSELMLGGTNTLVLHN
          ..F..S..VSKSNVVDDM.Q..PVLY.PGEEPD.C.VIKY.PY.GD.KRALDE.T.ELMLG.TNTLVLHN
Retrocopy SLFP<SEAVSKSNVVDDMAQRHPVLYAPGEEPDRCAVIKYMPYAGDPKRALDESTLELMLGVTNTLVLHN

Parental  TCEDSLLAAPIMLDLALLTELCQRVSFCTDMDPEPQTFHPVLSLLSF-LFKAPLVPPGSPVVNALFRQRS
          TCEDSLLAAPI.LDLALLTELC..VSFCT....EPQTFHP..SLLS..LFK...VPPGSPVV.ALFRQ.S
Retrocopy TCEDSLLAAPIILDLALLTELCHCVSFCTNDNTEPQTFHPMPSLLSI<LFK---VPPGSPVVSALFRQLS

Parental  CIENILRACVGLPPQNHMLLEHKMERPGPSLKRVGPVAATYPVLNKKGPVPTATNGCTGDANGHLQ-EEP
          CIENI.RACVGLPPQNH..L.HKME.P.P.LK.VGPVAA..PVLNKKGPVP.ATNGCT.D.NGH.Q.EEP
Retrocopy CIENIHRACVGLPPQNHVVLVHKMELPVPGLK*VGPVAAACPVLNKKGPVPAATNGCTSDTNGHPQVEEP

Parental  PMPTT
          .M.TT
Retrocopy QMHTT

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	0.05 RPM	17.50 RPM
SRP007412_cerebellum	0.00 RPM	15.17 RPM
SRP007412_heart	0.00 RPM	16.10 RPM
SRP007412_kidney	0.00 RPM	29.32 RPM
SRP007412_liver	0.00 RPM	12.87 RPM
SRP007412_testis	1.04 RPM	162.24 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_2019 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2019 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2918

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014230	6 retrocopies	retro_cjac_2768, retro_cjac_2803, retro_cjac_2809, retro_cjac_2831, retro_cjac_3817, retro_cjac_435,
Homo sapiens	ENSG00000105655	1 retrocopy	retro_hsap_2918,
Gorilla gorilla	ENSGGOG00000016939	1 retrocopy	retro_ggor_2019 ,
Nomascus leucogenys	ENSNLEG00000006026	1 retrocopy	retro_nleu_826,