RetrogeneDB ID: retro_pabe_1488

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:25419239..25419728(-)
• 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_1488
CTGAGTGAGTGCCTGATCCGCCACCAGGAGGAGCTGGGCAACGAGTCCAACTTCAGTGATGCACTGCTCGATGCCAGTGA
GTCCATGAAGCACCTGGCAGAGGTGAAGTACTCCCTGGACATAGAGGTCAAGCAGAACTTCATTGACCTCCTCCAGAACC
TGTGTGAGAAAGACCTGAAGGGGATCCCGCACCACCTGCAGAAGCTGGACGGCCGCCGCCTGGACTTAGAATAAAAGAAG
TGGCAGGGCAAGAGCCCCGATGAGGAGCTGTGCCAGGCACTGGAGAAGTTTGAGGACTCCAAGGAGGTGGAAGAAACCAG
CATGCACAACCTCCTGGACACCAACATTGAGCAGGTGAGTCAACTCCCAGCCCTGGTAGAGGCGCAGCTGGACTACCATT
GGCAGGCTTTGCAGATCCTGGACGAGCTGACAGAGAAGCTCAAGCACAGGATGCGGAAATCTTCCTCACATCAAATATTT
GAAAAGAAA

Alignment

ORF - retro_pabe_1488 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.56 %
• Parental protein coverage: 53.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAEVLARTIEYL--QPNPGDALLDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLE
          ..E.L.R..E.L....N..DALLDA.ESMK.LAEVK.SLDIEVKQNFID.LQNLCEKDLK.I.HHL.KL.
Retrocopy LSECLIRHQEELGNESNFSDALLDASESMKHLAEVKYSLDIEVKQNFIDLLQNLCEKDLKGIPHHLQKLD

Parental  GRRLDFDYKKKRQGKIPDEELRQALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQI
          GRRLD...KK..QGK.PDEEL.QALEKFE.SKEV.ETSMHNLL.T.IEQVSQL.ALV.AQLDYH.QA.QI
Retrocopy GRRLDLE*KKW-QGKSPDEELCQALEKFEDSKEVEETSMHNLLDTNIEQVSQLPALVEAQLDYHWQALQI

Parental  LDELAEKLKRRMREASSRPKREYK
          LDEL.EKLK.RMR..SS....E.K
Retrocopy LDELTEKLKHRMRKSSSHQIFEKK

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	1.16 RPM	28.53 RPM
SRP007412_cerebellum	2.07 RPM	17.15 RPM
SRP007412_heart	0.36 RPM	5.06 RPM
SRP007412_kidney	0.76 RPM	29.07 RPM
SRP007412_liver	0.24 RPM	21.42 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1488 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1488 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1488 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,