RetrogeneDB ID: retro_pabe_1570

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 18:72673968..72674414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSPPYG00000012740
• Aliases: PLEKHB2, EVT2
• Description: Pleckstrin homology domain-containing family B member 2 [Source:UniProtKB/Swiss-Prot;Acc:Q5R4K6]

Sequence

>retro_pabe_1570
AAAGACTGCATGCTGCAGATTGTTTGCTCAGATGGGAAAGCAATTAGTCTTTGTGCAGAAAACACAGTGATTGCTTGGCC
TGGAAATTTACACTCCAAGATTCCAGGACAAACACAGACTATGTGGGCTCCACAGTCATGACTGATGAGGTACCCGTGGT
TTCCTCCCCTCCACCACACACGGCCTGTGCTGCACCGGCCACTGAGGAATAGGGCTATGAGCCATACAGAGGTGTGTGCC
TGCCAGGAACTCAAATTGTCTATGCTGCTAATGGACAGGCATATGCTGTGCTCTACCAGTACTCGTATGCAGGACTTTAT
GGACAGCAGTCTGCTAACCAAGTCATCATTCAAGAGTGATGTCGAGACAATGACAGTGACCTGGCAGTGGGCATGTTGGC
AGGAGTTGCCATGGTCATGGCCTTAGGGTCTCTATTCTTAGTCTTC

Alignment

ORF - retro_pabe_1570 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.15 %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KDCMLQIVCRDGKTISLCAEST-DDCLAWKFTLQDSRTNTAYVGSAVMTDETSMVSSPPPYTAYAAPAPE
          KDCMLQIVC.DGK.ISLCAE.T..DCLAWKFTLQDSRTNT.YVGS.VMTDE...VSSPPP.TA.AAPA.E
Retrocopy KDCMLQIVCSDGKAISLCAENT<SDCLAWKFTLQDSRTNTDYVGSTVMTDEVPVVSSPPPHTACAAPATE

Parental  QAYGYGPYGGAYPPGTQVVYAANGQAYAVPYQYPYAGLYGQQPANQVIIRERYRDNDSDLALGMLAGAAT
          ...GY.PY.G...PGTQ.VYAANGQAYAV.YQY.YAGLYGQQ.ANQVII.E..RDNDSDLA.GMLAG.A.
Retrocopy E*-GYEPYRGVCLPGTQIVYAANGQAYAVLYQYSYAGLYGQQSANQVIIQE*CRDNDSDLAVGMLAGVAM

Parental  GMALGSLFWVF
          .MALGSLF.VF
Retrocopy VMALGSLFLVF

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	0.00 RPM	263.74 RPM
SRP007412_cerebellum	0.00 RPM	230.92 RPM
SRP007412_heart	0.00 RPM	30.28 RPM
SRP007412_kidney	0.00 RPM	134.74 RPM
SRP007412_liver	0.00 RPM	25.92 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1570 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1570 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1570 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1890

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570 ,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,