RetrogeneDB ID: retro_ptro_2501

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 6:161189994..161191065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL3L
• Ensembl ID: ENSPTRG00000007617
• Aliases: None
• Description: ribosomal protein L3-like [Source:HGNC Symbol;Acc:10351]

Sequence

>retro_ptro_2501
TCCAAGCCGGTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGCATGACTCACATCGTGCGGGAAGTCGACAGGCCAGG
ATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTAGAGACACCACCCATGGTGGTTGTGGGCATTGTGG
GCTACGTGGAAACCCCTCGAGGCCTCCGGACCTTCAAGACTGTCTTTGCTGAGCACATCAGTGATGAATGCAAGAGGCGT
TTCTATAAGAATTGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACTGCAAGAAATGGCAGGATGAGGATGACAAGAA
GCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCCGTGTCATTGCCCACACCCAGATGCGCCTGC
TTCCTCTGCGCCAGAAGAAGGCCCACCTGATGGAGATCCAGGTGAACGGAGGCACCGTGGCCGAGAAGCTGGACTGGGCC
CGCGAGAGGCTCGAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGATGAGATGATCGACGTCATCGGGGTGACCAA
GGGCAAAGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAACCTGCCCCGCAAGACCCACCAAGGCCTGCGCAAGG
TGGCCTGTATTGGGGCATGGCATCCTGCTCGTGTAGCCTTCTCTGTGGCACGCGCTGGGCAGAAAGGCTACCATCACCGC
ACTGAGATCAACAAGAAGATCTATAAGATTGGCCAGGGCTACCTTATCAAGGATGGCAAGCTGATCAAGAACAATGCCTC
CACTGACTATGACCTATCTGACAAGAGCATCAACCCTCTGGGTGGCTTTGTCCACTATGGTGAAGTGACCAATGACTTTG
TCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGGGTGCTCACCCTCCGCAAGTCCTTGCTGGTGCAGACGAAGCGG
CGGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCATGGCCGCTTCCAGACCATGGAGGA
GAAGAAAGCATTCATGGGACCACTCAAGAAA

Alignment

ORF - retro_ptro_2501 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.31 %
• Parental protein coverage: 87.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQPVHLTAFLGYKAGMTHTLREVHRPGLKISKREEVEAVTIVETPPLMVVGVVGYVATPRGLRSFKTIFA
          S.PVHLTAFLGYKAGMTH..REV.RPG.K..K.E.VEAVTIVETPP..VVG.VGYV.TPRGLR.FKT.FA
Retrocopy SKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFA

Parental  EHLSDECRRRFYKDWHKSKKKAFTKACKRWRDTDGKKQLQKDFAAMKKYCKVIRVIVHTQMKLLPFRQKK
          EH.SDEC.RRFYK.WHKSKKKAFTK.CK.W.D.D.KKQL.KDF..MKKYC.VIRVI.HTQM.LLP.RQKK
Retrocopy EHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDDKKQLEKDFSSMKKYCQVIRVIAHTQMRLLPLRQKK

Parental  AHIMEIQLNGGTVAEKVAWAQARLEKQVPVHSVFSQSEVIDVIAVTKGRGVKGVTSRWHTKKLPRKTHKG
          AH.MEIQ.NGGTVAEK..WA..RLE.QVPV..VF.Q.E.IDVI.VTKG.G.KGVTSRWHTK.LPRKTH.G
Retrocopy AHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKNLPRKTHQG

Parental  LRKVACIGAWHPARVGCSIARAGQKGYHHRTELNKKIFRIGRGPHMEDGKPVKNNASTSYDVTAKSITPL
          LRKVACIGAWHPARV..S.ARAGQKGYHHRTE.NKKI..IG.G....DGK..KNNAST.YD...KSI.PL
Retrocopy LRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPL

Parental  GGFPHYGEVNNDFVMLKGCIAGTKKRVITLRKSLLVHHSRQAVENIELKFIDTTSKFGHGRFQTAQEKRA
          GGF.HYGEV.NDFVMLKGC..GTKKRV.TLRKSLLV...R.A.E.I.LKFIDTTSKFGHGRFQT..EK.A
Retrocopy GGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKA

Parental  FMGPQKK
          FMGP.KK
Retrocopy FMGPLKK

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	123.39 RPM	0.02 RPM
SRP007412_cerebellum	88.19 RPM	0.00 RPM
SRP007412_heart	25.68 RPM	38.27 RPM
SRP007412_kidney	149.98 RPM	0.00 RPM
SRP007412_liver	101.21 RPM	0.03 RPM
SRP007412_testis	21.18 RPM	0.84 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2501 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2501 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2501 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 25 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,
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,