RetrogeneDB ID: retro_pabe_252

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:69741541..69743212(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHOC2
• Ensembl ID: ENSPPYG00000002651
• Aliases: None
• Description: Leucine-rich repeat protein SHOC-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RAV5]

Sequence

>retro_pabe_252
ATGAGTAGTAGTTTAGGAAAAGAAAAAGACTCTAAAGAAAAAGATCCCAAAGTACCATCAGCCAAGGAAAGAGAAAAGGA
GGCAAAAGCCTCTGGAGGTTTTGGGAAAGAGAGCAAAGAAAAAGAACCTAAGACCAAAGGGAAAGATGCCAAAGATGGAA
AGAAGGACTCCAGTGCTGCCCAACCAGGGGTGGCATTTTCAGTTGACAATACGATTAAATGGCCAAACCCAGCACCTGGG
ACTAGAAAAAAATCCAGCAATGCAGAGGTGATTAAAGAGCTCAACAAATGCCGGGAAGAGAATTCCATGCGTTTGGACTT
ATCCAAGAGATCTATACACATATTGCCATCATCAATCAAAGAGTTGACTCAATTAACAGAACTTTATTTATACAGTAACA
AATTGCAGTCCCTCCCAGCAGAGGTGGGATGTTTAGTAAATCTCATGACACTGGCTCTAAGTGAAAATTCACTTACCAGT
TTGCCTGACTCTCTTGATAACTTGAAGAAGCTGCGGATGCTTGATTTACGGCATAATAAACTGAGAGAAATTCCTTCAGT
GGTGTATAGGCTGGATTCTCTCACCACTCTTTACCTTCGCTTTAATCGTATAACTACTGTGGAAAAGGACATCAAAAACT
TGTCAAAACTCAGCATGCTTAGCATTCGAGAGAACAAAATTAAACAACTACCTGCTGAAATTGGTGAATTATGTAACCTC
ATTACGCTGGATGTAGCTCACAATCAACTTGAACACCTTCCAAAGGAGATTGGAAACTGTACACAGATAACCAACCTTGA
CTTGCAGCACAATGAACTGCTAGACCTCCCAGATACTATAGGAAACCTGTCCAGTTTAAGTCGTCTTGGTCTGAGATATA
ACAGACTGTCAGCAATACCCAGATCATTAGCAAAATGCAGTGCACTTGAAGAATTAAATTTAGAGAACAATAACATTTCT
ACTTTACCAGAGAGTCTTTTATCAAGTCTTGTGAAACTGAATAGTTTGACCTTAGCTAGAAATTGCTTCCAGTTATATCC
AGTGGGTGGTCCATCTCAGTTTTCTACCATCTATTCCCTCAACATGGAACACAATTGAATAAATAAAATTCCATTTGGAA
TTTTCTCCAGAGCAAAAGTATTAAGTAAGCTGAATATGAAGGACAATCAGTTAACATCACTTCCCTTGGATTTTGGAACT
TGGACCAGTATGGTAGAATTAAATTTAGCCACTAATCAGCTCACAAAGATCCCTGAGGATGTGTCCGGTCTCGTTTCTCT
TGAGGTTCTTATCTTATCAAACAATCTTCTAAAGAAGCTTCCCCATGGTCTTGGAAACCTTAGGAAGTTAAGAGAGTTGG
ATCTAGAAGAGAACAAATTGGAATCCTTGCCAAATGAAATTGCATATCTTAAGGATTTACAGAAATTAGTCTTGACAAAC
AACCAGTTGACCACTCTTCCCAGAGGCATTGGTCACCTTACTAATCTCACACATCTGGGCCTTGGAGAGAACCTACTTAC
TCACCTTCCTGAAGAAATTGGTACACTGGAGAACCTAGAAGGACTGTATTTGAATGACAAGCCCAACCTGCATAGCCTTC
CCTTTGAGCTGGCACTTTTAACGAAGCTTTCAATCATGAGTATTGAGAACTGTCCACTCAGTCACCTTCCA

Alignment

ORF - retro_pabe_252 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.92 %
• Parental protein coverage: 95.7 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSSLGKEKDSKEKDPKVPSAKEREKEAKASGGFGKESKEKEPKTKGKDAKDGKKDSSAAQPGVAFSVDN
          MSSSLGKEKDSKEKDPKVPSAKEREKEAKASGGFGKESKEKEPKTKGKDAKDGKKDSSAAQPGVAFSVDN
Retrocopy MSSSLGKEKDSKEKDPKVPSAKEREKEAKASGGFGKESKEKEPKTKGKDAKDGKKDSSAAQPGVAFSVDN

Parental  TIKRPNPAPGTRKKSSNAEVIKELNKCREENSMRLDLSKRSIHILPSSIKELTQLTELYLYSNKLQSLPA
          TIK.PNPAPGTRKKSSNAEVIKELNKCREENSMRLDLSKRSIHILPSSIKELTQLTELYLYSNKLQSLPA
Retrocopy TIKWPNPAPGTRKKSSNAEVIKELNKCREENSMRLDLSKRSIHILPSSIKELTQLTELYLYSNKLQSLPA

Parental  EVGCLVNLMTLALSENSLTSLPDSLDNLKKLRMLDLRHNKLREIPSVVYRLDSLTTLYLRFNRITTVEKD
          EVGCLVNLMTLALSENSLTSLPDSLDNLKKLRMLDLRHNKLREIPSVVYRLDSLTTLYLRFNRITTVEKD
Retrocopy EVGCLVNLMTLALSENSLTSLPDSLDNLKKLRMLDLRHNKLREIPSVVYRLDSLTTLYLRFNRITTVEKD

Parental  IKNLSKLSMLSIRENKIKQLPAEIGELCNLITLDVAHNQLEHLPKEIGNCTQITNLDLQHNELLDLPDTI
          IKNLSKLSMLSIRENKIKQLPAEIGELCNLITLDVAHNQLEHLPKEIGNCTQITNLDLQHNELLDLPDTI
Retrocopy IKNLSKLSMLSIRENKIKQLPAEIGELCNLITLDVAHNQLEHLPKEIGNCTQITNLDLQHNELLDLPDTI

Parental  GNLSSLSRLGLRYNRLSAIPRSLAKCSALEELNLENNNISTLPESLLSSLVKLNSLTLARNCFQLYPVGG
          GNLSSLSRLGLRYNRLSAIPRSLAKCSALEELNLENNNISTLPESLLSSLVKLNSLTLARNCFQLYPVGG
Retrocopy GNLSSLSRLGLRYNRLSAIPRSLAKCSALEELNLENNNISTLPESLLSSLVKLNSLTLARNCFQLYPVGG

Parental  PSQFSTIYSLNMEHNRINKIPFGIFSRAKVLSKLNMKDNQLTSLPLDFGTWTSMVELNLATNQLTKIPED
          PSQFSTIYSLNMEHN.INKIPFGIFSRAKVLSKLNMKDNQLTSLPLDFGTWTSMVELNLATNQLTKIPED
Retrocopy PSQFSTIYSLNMEHN*INKIPFGIFSRAKVLSKLNMKDNQLTSLPLDFGTWTSMVELNLATNQLTKIPED

Parental  VSGLVSLEVLILSNNLLKKLPHGLGNLRKLRELDLEENKLESLPNEIAYLKDLQKLVLTNNQLTTLPRGI
          VSGLVSLEVLILSNNLLKKLPHGLGNLRKLRELDLEENKLESLPNEIAYLKDLQKLVLTNNQLTTLPRGI
Retrocopy VSGLVSLEVLILSNNLLKKLPHGLGNLRKLRELDLEENKLESLPNEIAYLKDLQKLVLTNNQLTTLPRGI

Parental  GHLTNLTHLGLGENLLTHLPEEIGTLENLEELYLNDNPNLHSLPFELALCSKLSIMSIENCPLSHLP
          GHLTNLTHLGLGENLLTHLPEEIGTLENLE.LYLND.PNLHSLPFELAL..KLSIMSIENCPLSHLP
Retrocopy GHLTNLTHLGLGENLLTHLPEEIGTLENLEGLYLNDKPNLHSLPFELALLTKLSIMSIENCPLSHLP

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	15.65 RPM
SRP007412_cerebellum	0.00 RPM	14.35 RPM
SRP007412_heart	0.03 RPM	7.56 RPM
SRP007412_kidney	0.00 RPM	7.36 RPM
SRP007412_liver	0.03 RPM	6.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_252 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_252 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_252 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000013811	1 retrocopy	retro_mluc_690,
Oryctolagus cuniculus	ENSOCUG00000014348	1 retrocopy	retro_ocun_1369,
Pongo abelii	ENSPPYG00000002651	1 retrocopy	retro_pabe_252 ,
Pongo abelii	ENSPPYG00000013932	1 retrocopy	retro_pabe_2124,