RetrogeneDB ID: retro_ptro_1751

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 2B:239090725..239091949(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSPTRG00000021662
• Aliases: MSL3, MSL3L1
• Description: male-specific lethal 3 homolog (Drosophila) [Source:HGNC Symbol;Acc:7370]

Sequence

>retro_ptro_1751
TTAAAAGGCCTCTCCATCGAAGAAAAAAATGAAAATGATGAAAACTCATTAAGCAGTTCCTCCGACAGCAGTGAAGACAA
GGATGAAAAAATAAGTGAAGAATGTGATATTGAAGAAAAGACTGAAGTGAAAGAAGAACCGGAGCTTCAAACCAAAAGGG
AAATGGAAGAAAGAACAGTAACTCTAGAAATCCCTGAAGTTCTGAAGAGGCAGCTGGAGGATGATTGTTACTACATTAAT
CGGAGGAAACGGTTAGTGCAACTTCCATGCCACACCAACATCATAACGATTTTGGAATCCTATGTGAAGCATTTTGCTAT
CAGTGCAGCCTTTTCAGCCAATGAGAGGCCTCGTCACCATCACGCTATGCCACATGCCAGCATGAACGTGCCTTATATCC
CAGCAGAAAAGAATGTTGACCTTTGTAAGGAGATGGTGGATGGATTAAGAATAACCTTTGATTACACTCTCCCGTTGGTT
TTACTCTATCCCTATGAACAAGCTCAGTATAAAAAGGTGACTGCATCTAAGGTTTTTCTTGCAATTAAGGAAAGTGCCAC
AAATACTAATAGGAGCCAGGAGACGCTCTCTCCCAGCTTACGTTTGTTGAATCCATCCAGGCCGCAGTCTGCAGAGAGTC
AGTCGACCAGCGGTGAACCAGCCACCCCCAAAAGGCGCAAAGCCGAGCCGCAAGCAGTGCAGTCTCTGAGGCGGTCCTCG
CCCCACACCGCCAACTGTGACAGGCTTTCTAAGAGCAGCACCTCACCTCAGCCCAAGCGCTGGCAGCAGGACATGTCCAC
CAGTGTGCCCAAGCTGTTCCTGCACCTGGAAAAGAAGACACCTGTGCATAGCAGATCATCTTCACCTACTCCTCTGACTC
CTAGCCAGGAAGGGAGTCCTGTGTTTGCTGGCTTTGAAGGGAGAAGAACTAATGAAATAAATGAGGTCCTCTCCTGGAAG
CTCGTACCTGACAATTACCCACCAGGTGACCAGCCACCTCCACCCTCTTACATTTACGGGGCGCAACATTTGCTGCGATT
GTTTGTCAAACTTCCAGAAATTCTTGGAAAAATGTCCTTTACTGAGAAGAATCTGAAGGCTTTATTGAAGCACTTTGATC
TCTTTGTGAGGTTTTTAGCAGAATACCACGATGACTTCTTCCCAGAGTCAGCTTACGTCGCTGCCTCTGAGGTGCATTAC
AGCACCAGGAACCCCCAGGCAGTC

Alignment

ORF - retro_ptro_1751 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.99 %
• Parental protein coverage: 78.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKGLPTEEKDENDENSLSSSSDCSENKDEEISEESDIEEKTEVKEEPELQTRREMEERTITIEIPEVLKK
          LKGL..EEK.ENDENSLSSSSD.SE.KDE.ISEE.DIEEKTEVKEEPELQT.REMEERT.T.EIPEVLK.
Retrocopy LKGLSIEEKNENDENSLSSSSDSSEDKDEKISEECDIEEKTEVKEEPELQTKREMEERTVTLEIPEVLKR

Parental  QLEDDCYYINRRKRLVKLPCQTNIITILESYVKHFAINAAFSANERPRHHHVMPHANMNVHYIPAEKNVD
          QLEDDCYYINRRKRLV.LPC.TNIITILESYVKHFAI.AAFSANERPRHHH.MPHA.MNV.YIPAEKNVD
Retrocopy QLEDDCYYINRRKRLVQLPCHTNIITILESYVKHFAISAAFSANERPRHHHAMPHASMNVPYIPAEKNVD

Parental  LCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTSSKFFLPIKESATSTNRSQEELSPSPPLLNPSTPQS
          LCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVT.SK.FL.IKESAT.TNRSQE.LSPS..LLNPS.PQS
Retrocopy LCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVTASKVFLAIKESATNTNRSQETLSPSLRLLNPSRPQS

Parental  TESQPTTGEPATPKRRKAEPEALQSLRRSTRHSANCDRLSESSASPQPKRRQQDTSASMPKLFLHLEKKT
          .ESQ.T.GEPATPKRRKAEP.A.QSLRRS..H.ANCDRLS.SS.SPQPKR.QQD.S.S.PKLFLHLEKKT
Retrocopy AESQSTSGEPATPKRRKAEPQAVQSLRRSSPHTANCDRLSKSSTSPQPKRWQQDMSTSVPKLFLHLEKKT

Parental  PVHSRSSSPIPLTPSKEGSAVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVK
          PVHSRSSSP.PLTPS.EGS.VFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVK
Retrocopy PVHSRSSSPTPLTPSQEGSPVFAGFEGRRTNEINEVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVK

Parental  LPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHDDFFPESAYVAACEAHYSTKNPRAI
          LPEILGKMSF.EKNLKALLKHFDLF.RFLAEYHDDFFPESAYVAA.E.HYST.NP.A.
Retrocopy LPEILGKMSFTEKNLKALLKHFDLFVRFLAEYHDDFFPESAYVAASEVHYSTRNPQAV

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	1.91 RPM	18.12 RPM
SRP007412_cerebellum	0.79 RPM	21.11 RPM
SRP007412_heart	1.72 RPM	8.07 RPM
SRP007412_kidney	1.23 RPM	14.15 RPM
SRP007412_liver	1.67 RPM	11.92 RPM
SRP007412_testis	72.82 RPM	34.78 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1751 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1751 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1751 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2401
Gorilla gorilla	retro_ggor_1820
Pongo abelii	retro_pabe_2166

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009278	1 retrocopy	retro_btau_883,
Callithrix jacchus	ENSCJAG00000001061	1 retrocopy	retro_cjac_1490,
Cavia porcellus	ENSCPOG00000004692	5 retrocopies	retro_cpor_1423, retro_cpor_1424, retro_cpor_1425, retro_cpor_1426, retro_cpor_95,
Homo sapiens	ENSG00000005302	2 retrocopies	retro_hsap_2401, retro_hsap_4097,
Gorilla gorilla	ENSGGOG00000006582	2 retrocopies	retro_ggor_1820, retro_ggor_2749,
Macaca mulatta	ENSMMUG00000002689	2 retrocopies	retro_mmul_2362, retro_mmul_972,
Monodelphis domestica	ENSMODG00000017350	1 retrocopy	retro_mdom_1422,
Pongo abelii	ENSPPYG00000020123	2 retrocopies	retro_pabe_2166, retro_pabe_3353,
Pan troglodytes	ENSPTRG00000021662	2 retrocopies	retro_ptro_1751 , retro_ptro_2778,
Pteropus vampyrus	ENSPVAG00000005000	1 retrocopy	retro_pvam_203,
Sorex araneus	ENSSARG00000008477	1 retrocopy	retro_sara_139,
Tarsius syrichta	ENSTSYG00000012788	4 retrocopies	retro_tsyr_1079, retro_tsyr_1649, retro_tsyr_1706, retro_tsyr_948,