RetrogeneDB ID: retro_pabe_3542

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:14904394..14905172(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL1
• Ensembl ID: ENSPPYG00000009405
• Aliases: None
• Description: SH3-domain GRB2-like 1 [Source:HGNC Symbol;Acc:10830]

Sequence

>retro_pabe_3542
GAGTCCAACTTCAGCGATGCACTGCTGGATGCCGGCGAGCCCATGAAGCGCCTGGCAGAGGTGAAGGACTCCCTGGACAC
AGAGGTCAAGCATAACTTCATTGATCCCCTCCAGAACCTATGCAAGAAAGACCTGAAGGAGATCCAGCACCACCTGCAGA
AGCTGGAGGGCCACCACCTGGACTTTGACTAAAAGAAGCGGCAGGGCAAGATCCCCAATGAGGAGCTGCATCAGGTGCTG
GAGAAGTTTGAACAGTCCAAGGAGGTGGCAGAAACCAGCATGCACAACCTCCTGGAGACCGACATCCAGTAGGTGAGTCA
ACTCCCGGCCTTGGTGGAGGTGCAGCTGGACTACCACCGGCAGGCCGCGCAGATCCTGGACGAGCTGGCCCAGAAGCTCA
AGTGCAGAATCCGGGAAGCTTCCTCACAACCCAAGCGGGAGTATAAGCCCAAGCCCCGGGAGTGCTTTGACCTCAAAAGC
CTGAGCAGTCCAACCGGGGCTTCTCCTGCACCACAGTCCCCAAGATCGCAGCTTCGTCCTCTTTCCGATCTTACGACAAG
TCCATCTGGACTCCTAGCAGGAGCATGCCGCCCCTAGACCAGCGAGCTGCAAGGTGCTGTATGACTTGGAGCTGGGGAAA
GATAGGGAGCTGGGCTTCCATGAGGGCGATGTCTTCACGCTGATCAACCAGATGAACGAGAACTGATACGAGGGCATGCT
GGATGGCCAGTCGCGCTTCTTCCTGCTCAGCTATGTGGACGTGCTTGTGCCTCTGCCC

Alignment

ORF - retro_pabe_3542 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.47 %
• Parental protein coverage: 85.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QPNPGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQG
          ..N..DALLDAGE.MKRLAEVKDSLD.EVK.NFIDPLQNLC.KDLKEIQHHL.KLEG..LDFD.KK.RQG
Retrocopy ESNFSDALLDAGEPMKRLAEVKDSLDTEVKHNFIDPLQNLCKKDLKEIQHHLQKLEGHHLDFD*KK-RQG

Parental  KIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRRMRE
          KIP.EEL.Q.LEKFE.SKEVAETSMHNLLETDI..VSQL.ALV..QLDYHRQA.QILDELA.KLK.R.RE
Retrocopy KIPNEELHQVLEKFEQSKEVAETSMHNLLETDIQ*VSQLPALVEVQLDYHRQAAQILDELAQKLKCRIRE

Parental  ASSRPKREYKPKPREPFDL-GEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQ-PSCKAL
          ASS.PKREYKPKPRE.FDL...PEQSN.GF.CTT.PKIAASSSFRS.DK.I.TPSRSMPPLDQ..SCK.L
Retrocopy ASSQPKREYKPKPRECFDL<QKPEQSNRGFSCTTVPKIAASSSFRSYDKSIWTPSRSMPPLDQ<ASCKVL

Parental  YDFEPENDGELGFREGDVITLTNQIDENWYEGMLDGQSGFFPLSYVEVLVPLP
          YD.E...D.ELGF.EGDV.TL.NQ..EN.YEGMLDGQS.FF.LSYV.VLVPLP
Retrocopy YDLELGKDRELGFHEGDVFTLINQMNEN*YEGMLDGQSRFFLLSYVDVLVPLP

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	0.72 RPM	28.53 RPM
SRP007412_cerebellum	2.19 RPM	17.15 RPM
SRP007412_heart	0.42 RPM	5.06 RPM
SRP007412_kidney	0.96 RPM	29.07 RPM
SRP007412_liver	0.21 RPM	21.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3542 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3542 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3542 has 0 orthologous retrocopies within eutheria group .

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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 ,