RetrogeneDB ID: retro_pabe_2683

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:129473124..129474169(+)
• Located in intron of: ENSPPYG00000015739

Retrocopy information

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

Parental gene information

• Parental gene symbol: KDELC1
• Ensembl ID: ENSPPYG00000005483
• Aliases: None
• Description: KDEL (Lys-Asp-Glu-Leu) containing 1 [Source:HGNC Symbol;Acc:19350]

Sequence

>retro_pabe_2683
GAAACCATTGCTCAGATTCAGAGAGATCCGGCACATTTCCCTACTGTGGATCCAGAAAAGATTGCAGTAGGAATCCCAAA
AAGACTTGGACAGAGGCAGAGCCTGTGTCACTACACCTTAAAAGATAACAAAGTTTATATCAAGACTCACGGTGAACATG
TAGGTTTTAGAATTTTCATGGATGCCGTACTACTTCCTTTGACTAGAAAGGTGAAGATGCCAGATATAGAGTTCTTTAAT
TTGGCAGACTGGCCTTTTCTTTGGAAAAAAAGAAATCCAATTCAAACATCCATCCGACCTTTTCCTGGTGTGGCTCCACA
GATTCGAAGGATATCGTGATGCCCACCTACTACTTGACTGACTCTGTTTTAGAAATCATGGGCCGGGTAAGTCTGGATAT
GATGTCTGTGCAAGCTAACACGGGTCCTCCCTGGGAAAGCAAAAACTCCACAGCTCTCTGGAGAGGGCGAGACAGCTGCA
AAGGAGACTTGAGTTGGTTAAACTCAGTAGAAACACCCTGAACTCATAGACGCTGCTTTCACCAACTTTTTCTTCTTTAA
ACATGATGAAAACCTGTATGGTCCCATTGCGAAACACATTTCATTTTTTGATTTCTTCAAGCATAAGTATCAAATAAATA
TTGATGGCATCTTAGCAGCTTATCACCTGCCATATTTACTAGTTAGTGACAGTGTTGTGCTGAAGCCAAGACTCCATCTA
CTATGAACATTTTTACAATGAGCTGCAGCCCTGGAAACACTACATTCCAGTGAAGAGCAACCTGAACAATCTGCTAGAAA
AACTTAAATGGGCAAAAGATCACAATGAAGAGGCCAAAAAGATAGCAAAAGCAGGACAAGAATTTGCAAGAAATAATCTC
ATGGATGATGACATATTCTGTTATTATTTCAAACTTTTCCAGGAATATGCCAATTTACAAGTGAGTGGGCCCCAAATCTG
AGAGGGCATGAAAAGGGTAGAACCACAGACTGAGAATGACCTCTTCCCTTGCACTTGCCATAGGAAAAAGACCAAAGATG
AACTC

Alignment

ORF - retro_pabe_2683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 69.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  ETIAQIQRDLAHFPAVDPEKIAVEIPQRFGQRQSLCHYTLKDNKVYIKTHGEHVGFRIFMDAILLSLTRK
          ETIAQIQRD.AHFP.VDPEKIAV.IP.R.GQRQSLCHYTLKDNKVYIKTHGEHVGFRIFMDA.LL.LTRK
Retrocopy ETIAQIQRDPAHFPTVDPEKIAVGIPKRLGQRQSLCHYTLKDNKVYIKTHGEHVGFRIFMDAVLLPLTRK

Parental  VKMPDVEFFVNLGDWPLEKKKSN-SN--IHPIFSWCGSTDSKDIVMPTYDLTDSVLETMGRVSLDMMSVQ
          VKMPD.EFF.NL.DWP...KK.N.SN..IHP.FSWCGSTDSKDIVMPTY.LTDSVLE.MGRVSLDMMSVQ
Retrocopy VKMPDIEFF-NLADWPFLWKKRN<SNSNIHPTFSWCGSTDSKDIVMPTYYLTDSVLEIMGRVSLDMMSVQ

Parental  ANTGPPWESKNSTAVWRGRDSRK-ERLELVKLSR-KHPELIDAAFTNFFFFKHDESLYGPIVKHISFFDF
          ANTGPPWESKNSTA.WRGRDS.K..RLELVKLSR.KHPELIDAAFTNFFFFKHDE.LYGPI.KHISFFDF
Retrocopy ANTGPPWESKNSTALWRGRDSCK<RRLELVKLSR<KHPELIDAAFTNFFFFKHDENLYGPIAKHISFFDF

Parental  FKHKYQINIDGTVAAYRLPYLLVGDSVVLK-QDSIYYEHFYNELQPWKHYIPVKSNLSDLLEQLKWAKDH
          FKHKYQINIDG..AAY.LPYLLV.DSVVLK.QDSIYYEHFYNELQPWKHYIPVKSNL..LLE.LKWAKDH
Retrocopy FKHKYQINIDGILAAYHLPYLLVSDSVVLK>QDSIYYEHFYNELQPWKHYIPVKSNLNNLLEKLKWAKDH

Parental  DEEAKKIAKAGQEFARNNLMGDDIFCYYFKLFQEYANLQVSEPQIREGMKRVEPQTEDDLFPCTCHRKKT
          .EEAKKIAKAGQEFARNNLM.DDIFCYYFKLFQEYANLQVS.PQI.EGMKRVEPQTE.DLFPCTCHRKKT
Retrocopy NEEAKKIAKAGQEFARNNLMDDDIFCYYFKLFQEYANLQVSGPQI*EGMKRVEPQTENDLFPCTCHRKKT

Parental  KDEL
          KDEL
Retrocopy KDEL

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	1.33 RPM
SRP007412_cerebellum	0.36 RPM	3.77 RPM
SRP007412_heart	0.03 RPM	1.41 RPM
SRP007412_kidney	0.07 RPM	2.78 RPM
SRP007412_liver	0.00 RPM	0.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2683 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2683 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2683 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007858	1 retrocopy	retro_nleu_954,
Pongo abelii	ENSPPYG00000005483	1 retrocopy	retro_pabe_2683 ,
Rattus norvegicus	ENSRNOG00000011740	1 retrocopy	retro_rnor_823,