RetrogeneDB ID: retro_pabe_2854

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 6:31848704..31849887(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSPPYG00000006973
• Aliases: None
• Description: ribosomal protein L3-like [Source:HGNC Symbol;Acc:10351]

Sequence

>retro_pabe_2854
TCTCACAGAAAGTTCTCCACTCCCAGACATGGGTCCCTCAGCTTTCTGCCTTGGAAGCGCAGCAGCAGGCATCGTGGGAA
GGTGAAGAGCTTCCCTAAGGATGACCCGTCCAAGCCGGTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGCATGACCC
ACATCGTGCGGGAAGTCGACAGGCCAGGATCCAAGGTGAAAAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTGGAGAGG
CCACCCATGGTGGTTGTGGGCATTGTGGGCTATGTGGAAACCCCTCAAGGCCTCCGGACTTGCAAGACTGTCTTCGCTGA
GCACATCAGTGATGAATGCAAGAGGCATTTCTATAAGAACTGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACTGCA
AGAAATGGCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCTGC
GTCATTGCCCACACCCAGATGCGCCTGCTTCCTCTGCACCAGAAGAAGGCCCACCTGATGGAGATCCAGGTGAACGGAGG
CACTGTGGCTGAGAAGCTGGACTGGGCTGGCGAGAGGCTCAAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGATG
AGATGATCGACGTCATCAGGGTGATCAAGGGCAAAGGCTACAAAGGGGTCACCAGTCATTGGCACACCAAGAAGCTGCCC
TGCAAGACCCACCGAGGCTTGCACAAGGTGGCCTGTATTGGGGCATGGCATCCTGCTCGTGTGGGCTTCTCTGTGGTACG
CGCTGGGCAGAAAGGCTACCATCACCGCACTGAGATCAACAAGAAGATCTATAAGATTGGCCAGGGCTACCTACCTTATC
AAGGACGGCAAGCTGATCAAGAACAATGCCTCCACTGACTATGACCTGTCTGACAAGAGCATCAACCCTTTGGGTGGCTT
TGTCTACTACGGTGAAGTGACCAATGACTTTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGGGTGCTCACCC
TCCGCAAGTCCTTGCTGGTGCAGACAAAGCAGCGGGCTCTGGAGAAGATTGACTTTAAGTTCATTGACATCACCTCCAAG
TTTGGCCATGGCTGCTTCCAGACCATGGAGGAGAAGAAAGCATTCATGGGACCACTCAAGAAA

Alignment

ORF - retro_pabe_2854 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.9 %
• Parental protein coverage: 96.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SHRKFSAPRHGHLGFLPHKRSRRHRGKVKTWPRDDPSQPVHLTAFLGYKAGMTHTLREVHRPGLKISKRE
          SHRKFS.PRHG.L.FLP.KRS.RHRGKVK..P.DDPS.PVHLTAFLGYKAGMTH..REV.RPG.K..K.E
Retrocopy SHRKFSTPRHGSLSFLPWKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVDRPGSKVKKKE

Parental  EVEAVTIVETPPLVVVGVVGYVATPRGLRSFKTIFAEHLSDECRRRFYKDWHKSKKKAFSKACKRWRDPD
          .VEAVTIVE.PP.VVVG.VGYV.TP.GLR..KT.FAEH.SDEC.R.FYK.WHKSKKKAF.K.CK.W.D.D
Retrocopy VVEAVTIVERPPMVVVGIVGYVETPQGLRTCKTVFAEHISDECKRHFYKNWHKSKKKAFTKYCKKWQDED

Parental  GKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKKAHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSVF
          GKKQL.KDF..MKKYC.VI.VI.HTQM.LLP..QKKAH.MEIQ.NGGTVAEK..WA..RL..QVPV..VF
Retrocopy GKKQLEKDFSSMKKYCQVICVIAHTQMRLLPLHQKKAHLMEIQVNGGTVAEKLDWAGERLKQQVPVNQVF

Parental  SQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKGLRKVACIGAWHPARVGCSIARAGQKGYHHRTELN
          .Q.E.IDVI.V.KG.G.KGVTS.WHTKKLP.KTH.GL.KVACIGAWHPARVG.S..RAGQKGYHHRTE.N
Retrocopy GQDEMIDVIRVIKGKGYKGVTSHWHTKKLPCKTHRGLHKVACIGAWHPARVGFSVVRAGQKGYHHRTEIN

Parental  KKIY-RIGRGPHM-EDGKLVKNNASTSYDVTAKAITPLGGFPHYGEVNNDFVMLKGLIAGTKKRVITLRK
          KKIY.R..R......DGKL.KNNAST.YD...K.I.PLGGF..YGEV.NDFVMLKG...GTKKRV.TLRK
Retrocopy KKIY>RLARATYLIKDGKLIKNNASTDYDLSDKSINPLGGFVYYGEVTNDFVMLKGCVVGTKKRVLTLRK

Parental  RLAVAWXXXXXXXXXXKFIDTTSKFGHGRFQTAQEKRAFMGPQKK
          .L.V............KFID.TSKFGHG.FQT..EK.AFMGP.KK
Retrocopy SLLVQTKQRALEKIDFKFIDITSKFGHGCFQTMEEKKAFMGPLKK

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	0.44 RPM	0.06 RPM
SRP007412_cerebellum	1.09 RPM	0.00 RPM
SRP007412_heart	0.45 RPM	39.53 RPM
SRP007412_kidney	2.15 RPM	0.60 RPM
SRP007412_liver	1.38 RPM	0.34 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2854 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2854 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2854 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008489	1 retrocopy	retro_amel_1881,
Nomascus leucogenys	ENSNLEG00000008850	9 retrocopies	retro_nleu_1107, retro_nleu_1130, retro_nleu_1249, retro_nleu_1305, retro_nleu_1673, retro_nleu_1824, retro_nleu_2046, retro_nleu_2060, retro_nleu_3126,
Pongo abelii	ENSPPYG00000006973	1 retrocopy	retro_pabe_2854 ,
Pongo abelii	ENSPPYG00000011837	10 retrocopies	retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Pan troglodytes	ENSPTRG00000007617	12 retrocopies	retro_ptro_1439, retro_ptro_1473, retro_ptro_1753, retro_ptro_2150, retro_ptro_2339, retro_ptro_2462, retro_ptro_2501, retro_ptro_2646, retro_ptro_2741, retro_ptro_2767, retro_ptro_3163, retro_ptro_916,
Ictidomys tridecemlineatus	ENSSTOG00000012921	2 retrocopies	retro_itri_1344, retro_itri_867,