RetrogeneDB ID: retro_pabe_2166

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 2b:126314854..126316182(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSL3
• Ensembl ID: ENSPPYG00000020123
• Aliases: MSL3, MSL3L1
• Description: Male-specific lethal 3 homolog [Source:UniProtKB/Swiss-Prot;Acc:Q5R6Y9]

Sequence

>retro_pabe_2166
CGTAGATTACAGCATAAATTGGCAAGAAAAGCTGTAGCTCACCTGAGGAGCAAGAGAGAAAGAAGCAGCCGCTCCAGGTT
GCCTGGTGCTGACTCTGTCTTTTTTTAAAAGGCCTCTCCATCGAAGAAAAAGATGAGAATGATGAAAACTCATTAAGCAG
TTCCTCTGACAGTAGTGAAGACAAGGATGAAAAAATAAGTGAAGAAAGTGATATTGAAGAAAAGACTGAAGTGAAAGAAG
AACTGGAGCTTCAAACAAAAAGGGAAATGGAAGAAAGAACAGTAACTCTAGAAATCCCTGAAGTTCTGAAGAGGCAGCTG
GAGGATGATTGTTACTACATTAATCGGAGGAAACGGTTAGTGCAACTTCCATGCCACACCAACATCATAACGATTTTGGA
ATCCTATGTGAAGCATTTTGCTATCAGTGCAGCCTTTTCAGCCAATGAGAGGCCTCGTCACCATCACACTATGCCACATG
CCAGCATGAACGTGCCTTATATCCCAGCAGAAAAGAATGTTGACCTTTGTAAGGAGATGGTGGATGGATTAAGAATAACC
TTTGATTACACTCTCCCGTTGGTTTTACTCTATCCCTGTGAACAAGCTCAGTATAGAAAGGTGACTTCATCTAAGGTTTT
TCTTGCAATTAAGGAAAGTGCCACAAATACTAATAGGAGCCAGGAGAAGCTCTCTCCCAGCCCACGTTTGTTGAATCCAT
CCAGGCCGCAGTCTACAGAGAGTCAGTCGACCAGCGGTGAACCAGCCACCCCCAAAAGGCGCAAAGCCGAGCTGCAAGCA
GTGCAGTCTCTGAGACGGTCCTCGCCCCACACCGCCAACTGTGACAGGCTTTTTAAGAGCAGCACCTCACCTCAGCCCAA
GCGCTGGCAGCAGGACATGTCCACCAGCATGCCCAAGCTGTTCTTGCACCTGGAAAAGAAGACACCTGTGCATAGCAGAT
CATCTTCACCTATTCCTCTGACTCCTAGCCAGGAAGGGAGTCCTGTGTTTGCTGGCTTTGAAGGGAGAAGAACTAATGAA
ATAAATGAGGTCCTCTCCTGGAAGCTCGTACCTGACAATTACCCACCAGGCGACCAGCCACCTCCACCCTCTTACATTTA
CGGGGCGCAACATTTGCTGCGATTGTTTGTAAAACTTCCAGAAATTCTTGGAAAAATGTCCTTTACTGAGAAGAATCTGA
AGGCTTTATTGAAGCACTTTGATCTCTTTGTGAGGTTCTTAGCAGAATACCACGATGACTTCTTCCCAGAGTCAGCTTAC
GTCGCTGCCTCTGAGGTGCATTATAGCACCAAGAACCCCCAGGCAGTC

Alignment

ORF - retro_pabe_2166 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.26 %
• Parental protein coverage: 84.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RRLQRKLARKAVARLRSTGRKKKRCRLPGVDSVL--KGLPT-EEKDENDENSLSSSSDCSENKDEEISEE
          RRLQ.KLARKAVA.LRS......R.RLPG.DSV...K..P..EEKDENDENSLSSSSD.SE.KDE.ISEE
Retrocopy RRLQHKLARKAVAHLRSKRERSSRSRLPGADSVFF*KASPS<EEKDENDENSLSSSSDSSEDKDEKISEE

Parental  SDIEEKTEVKEEPELQTRREMEERTITIEIPEVLKKQLEDDCYYINRRKRLVKLPCQTNIITILESYVKH
          SDIEEKTEVKEE.ELQT.REMEERT.T.EIPEVLK.QLEDDCYYINRRKRLV.LPC.TNIITILESYVKH
Retrocopy SDIEEKTEVKEELELQTKREMEERTVTLEIPEVLKRQLEDDCYYINRRKRLVQLPCHTNIITILESYVKH

Parental  FAINAAFSANERPRHHHVMPHANMNVHYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPYEQAQYKKVT
          FAI.AAFSANERPRHHH.MPHA.MNV.YIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYP.EQAQY.KVT
Retrocopy FAISAAFSANERPRHHHTMPHASMNVPYIPAEKNVDLCKEMVDGLRITFDYTLPLVLLYPCEQAQYRKVT

Parental  SSKFFLPIKESATSTNRSQEELSPSPPLLNPSTPQSTESQPTTGEPATPKRRKAEPEALQSLRRSTRHSA
          SSK.FL.IKESAT.TNRSQE.LSPSP.LLNPS.PQSTESQ.T.GEPATPKRRKAE..A.QSLRRS..H.A
Retrocopy SSKVFLAIKESATNTNRSQEKLSPSPRLLNPSRPQSTESQSTSGEPATPKRRKAELQAVQSLRRSSPHTA

Parental  NCDRLSESSASPQPKRRQQDTSGSMPKLFLHLEKKTPVHSRSSSPIPLTPSKEGSAVFAGFEGRRTNEIN
          NCDRL..SS.SPQPKR.QQD.S.SMPKLFLHLEKKTPVHSRSSSPIPLTPS.EGS.VFAGFEGRRTNEIN
Retrocopy NCDRLFKSSTSPQPKRWQQDMSTSMPKLFLHLEKKTPVHSRSSSPIPLTPSQEGSPVFAGFEGRRTNEIN

Parental  EVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVKLPEILGKMSFSEKNLKALLKHFDLFLRFLAEYHD
          EVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVKLPEILGKMSF.EKNLKALLKHFDLF.RFLAEYHD
Retrocopy EVLSWKLVPDNYPPGDQPPPPSYIYGAQHLLRLFVKLPEILGKMSFTEKNLKALLKHFDLFVRFLAEYHD

Parental  DFFPESAYVAACEAHYSTKNPRAI
          DFFPESAYVAA.E.HYSTKNP.A.
Retrocopy DFFPESAYVAASEVHYSTKNPQAV

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	0.06 RPM	29.86 RPM
SRP007412_cerebellum	0.12 RPM	14.96 RPM
SRP007412_heart	0.03 RPM	5.36 RPM
SRP007412_kidney	0.23 RPM	10.24 RPM
SRP007412_liver	0.34 RPM	8.17 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2166 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2166 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2166 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2401
Pan troglodytes	retro_ptro_1751
Gorilla gorilla	retro_ggor_1820

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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,