RetrogeneDB ID: retro_ggor_2151

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 5:15416503..15417357(+)
• 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_2151
GTGCAAGATCCGGGGCCAAGTGAAGAACCCCGGCTCCTGGGCGAGTGCCTGATCCGCCAAGGGAAGGAGCTACGCGATGA
GTCCAACTTCAGTGATGCACTGCTGGATGCCGGCGAGCCCATGAAGCACCTGGCAGAGGTGAAGGACTCCCTGGACATAG
AGGTCAAGCATAACTTCATTGACCCTCTCCAGAACCTATGCGAGAAAGACCTGAAGGAGATCCAGCACCACCTGCAGAAG
CTGGAGGGCCGCCGCCTGGACTTTGACTAAAAGAAGCGGCAGGGCAAGATCCCCGAAGAGGAGCTGCACCAGGCGCTGGA
GAAGTTTGAGGAGTCCAAGGAGGTGGCAGAAACCAGCATGCACAACCTCCTGGAGACCGACATCCAGTAGGTGAGTCAAC
TCCCAGCCTTCGTGGAGGCACAGCTGGACTACCACCGGCAGGCCGTGCAGATCCTGGACGAGCTGGCCCAGAAGCTCAAG
TGCAGGATCCGGGAAGCTTCCTCACGACCCAGGCGGGAGTATAAGCCCAAGCCCCGGGAGTGCTTTGACCTCGGAAAGCC
TGAGCAGTCCAACCGGGGCTTCCCCTGCACCACAGTCCCCAAGATCGCAGCTTCGTCCTTCCGATCTTACGACAAGTCCA
TCTGGACTCCTAGCAGGAGCATGCTGCCCCTAGACCAGCCGAGCTGCAAGGGCTGTATGACTTGGAGCTGGAGAAAGATA
GGGAGCTGGGCTTCCATGAGGGCGATGTCTTCATGCTGATCAACCAGATGAACGAGAACTGATACGAGGGCATGCTGGAT
GGCCAGTCGGGCTTCTTCCTGCTCAGCTATGTGGACGTGCTCGTGCCTCTGCCC

Alignment

ORF - retro_ggor_2151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.9 %
• Parental protein coverage: 77.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKNPGYPQSEGLLGECMIRHGKELGGESNFGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKD
          V..PG......LLGEC.IR.GKEL..ESNF.DALLDAGE.MK.LAEVKDSLDIEVK.NFIDPLQNLCEKD
Retrocopy VQDPGPSEEPRLLGECLIRQGKELRDESNFSDALLDAGEPMKHLAEVKDSLDIEVKHNFIDPLQNLCEKD

Parental  LKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVD
          LKEIQHHL.KLEGRRLDFD.KK.RQGKIP.EEL.QALEKFEESKEVAETSMHNLLETDI..VSQL.A.V.
Retrocopy LKEIQHHLQKLEGRRLDFD*KK-RQGKIPEEELHQALEKFEESKEVAETSMHNLLETDIQ*VSQLPAFVE

Parental  AQLDYHRQAVQILDELAEKLKRRMREASSRPKREYKPKPREPLDLGEPEQSNGGFPCTTAPKIAASSSFR
          AQLDYHRQAVQILDELA.KLK.R.REASSRP.REYKPKPRE..DLG.PEQSN.GFPCTT.PKIAA.SSFR
Retrocopy AQLDYHRQAVQILDELAQKLKCRIREASSRPRREYKPKPRECFDLGKPEQSNRGFPCTTVPKIAA-SSFR

Parental  SSDKPIRTPSRSMPPLDQPSCK-ALYDFEPENDGELGFREGDVITLTNQIDENWYEGMLDGQSGFFPLSY
          S.DK.I.TPSRSM.PLDQPSCK..LYD.E.E.D.ELGF.EGDV..L.NQ..EN.YEGMLDGQSGFF.LSY
Retrocopy SYDKSIWTPSRSMLPLDQPSCK<GLYDLELEKDRELGFHEGDVFMLINQMNEN*YEGMLDGQSGFFLLSY

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	0.34 RPM	31.41 RPM
SRP007412_cerebellum	1.54 RPM	36.99 RPM
SRP007412_heart	0.31 RPM	11.54 RPM
SRP007412_kidney	0.57 RPM	19.63 RPM
SRP007412_liver	0.24 RPM	19.36 RPM
SRP007412_testis	0.41 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_2151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2151 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1859
Pongo abelii	retro_pabe_1516

---

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,