RetrogeneDB ID: retro_pabe_3575

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: Un:14751096..14752302(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ST6GAL1
• Ensembl ID: ENSPPYG00000014388
• Aliases: None
• Description: beta-galactoside alpha-2,6-sialyltransferase 1 [Source:RefSeq peptide;Acc:NP_001127059]

Sequence

>retro_pabe_3575
CTGGTTCACACCAACCTGCAGAAAAACTTCAGCTGCTGTGTCCTGGCCTTTCTCCTGCTTGCAGTCATCTGTGTGTGGAA
GAAAAAGAAGAAAGGGAATTACTATGATTCCCTTAAATTTCAAACCAAGAAGTTCCAGATGTTGAAAAATCTGGGGAAAG
TGGCCATGAGGTCTTATTCCCAATCTGCATCCTTACGCAGCACCCAGGACCCCGACAGGGGCAGCCAGGCCCTCAGCAAC
CCCAGAGGCCCAGCCAAGACTATCCAGAGGCCTCCTTCCAGGTATGGAACAAGGACAGCTTTTCCAAAAACCTTATCCCC
AGGCTGCAAACCATCTGGAAGAATTATTTAAGCATGAAAAAGTACAAAGTGTCCTAAAAGGGGCCAGGGCCCACCATTAA
GTTCAGTGCAGAGGCCCCACGCTGCCACCTCCTGGACCAAGTGAATGTATCCACAGTAGGGACCACAGATTTTCTCTTCA
GTACCTCTGAGTAGGAGAGTTACCTGCCCAAGGACAGCATTAGGACTGAGGCCAGGTCTTGGGGCAAGTGTGCTGTTTTC
TCATCAGCAAGATCTCTGAAGTCCTCGCAACTGGGCAGAGATCTAGATGATCATGATGCAGTCTTGAGGTTTAATGAGGC
ACCCACGGCCAACTTCCGTCAAGATGTAGCCACAAAAACAACCATTCGCCTGCTGAACTCTCAGTTGGTCACCACAAAAA
GGCATTTCCTCAAAGACAGTTTGTACAATGAAGGAATCCTAATTGTATGGGATGCATCTATATATCATTCAGGTATTTCA
AAGTGGTACCAGAATCCAGACTATAATTTCTTTAATAACTACAAGAGCTATCGTAAGCTGTACCCCAATCAGCCCTTTTA
CATCCTCAAGCCCCAGGTGCCTTGGGAGTTGTGGGACATCCTGCAAGAAATCTGCTCAGAAGAGATTCGGTGACGCCCCC
ATCCTCTGGGATACTTGGTGTCATGATCATGATGATGCTGTGTGACCAGGTAGGTATTAATGAGTTCCTCCCATCCAAGC
ATGAGACAGACTTGGGCTGCTACCACCAGCAGTTCTTCAATAGCGCCTGCACGATGGGCACCCACCACCTGCTGCTGTAT
TTGGTGAAGTGCCTCAATAAGGGCACAGATGAGGACATTTATCGCTTGGAAAAGCTACACTGCCTGGCTTCTGGGCCAAT
CACTGC

Alignment

ORF - retro_pabe_3575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.55 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MIHTNLKKKFSCCVLVFLLFAVICVWKEKKKGSYYDSFKLQTKEFQVLKSLGKLAMGSDSQSVSSSSTQD
          ..HTNL.K.FSCCVL.FLL.AVICVWK.KKKG.YYDS.K.QTK.FQ.LK.LGK.AM.S.SQS.S..STQD
Retrocopy LVHTNLQKNFSCCVLAFLLLAVICVWKKKKKGNYYDSLKFQTKKFQMLKNLGKVAMRSYSQSASLRSTQD

Parental  PHRGRQTLGSLRGLAKA-KPEASFPVWNKDSSSKNLIPRLQKIWKNYLSMNKYKVSYKGPGPGIKFSAEA
          P.RG.Q.L...RG.AK...PEASF.VWNKDS.SKNLIPRLQ.IWKNYLSM.KYKVS.KGPGP.IKFSAEA
Retrocopy PDRGSQALSNPRGPAKT<YPEASFQVWNKDSFSKNLIPRLQTIWKNYLSMKKYKVS*KGPGPTIKFSAEA

Parental  LRCHLWDYVNVSMVEATDFPFNTSEWEGYLPKESIRTKAGPWGRCAVVSSAGSLKSSQLGREIDDHDAVL
          .RCHL.D.VNVS.V..TDF.F.TSE.E.YLPK.SIRT.A..WG.CAV.SSA.SLKSSQLGR..DDHDAVL
Retrocopy PRCHLLDQVNVSTVGTTDFLFSTSE*ESYLPKDSIRTEARSWGKCAVFSSARSLKSSQLGRDLDDHDAVL

Parental  RFNGAPTANFQQDVGTKTTIRLMNSQLVTTEKRFLKDSLYNEGILIVWDPSVYHSDIPKWYQNPDYNFFN
          RFN.APTANF.QDV.TKTTIRL.NSQLVTT...FLKDSLYNEGILIVWD.S.YHS.I.KWYQNPDYNFFN
Retrocopy RFNEAPTANFRQDVATKTTIRLLNSQLVTTKRHFLKDSLYNEGILIVWDASIYHSGISKWYQNPDYNFFN

Parental  NYKSYRKLHPNQPFYILKPQMPWELWDILQEISPEEIQ-PNPPSSGMLGIIIMMTLCDQVDIYEFLPSKR
          NYKSYRKL.PNQPFYILKPQ.PWELWDILQEI..EEI....PPSSG.LG..IMM.LCDQV.I.EFLPSK.
Retrocopy NYKSYRKLYPNQPFYILKPQVPWELWDILQEICSEEIR<VTPPSSGILGVMIMMMLCDQVGINEFLPSKH

Parental  KTDVCYYYQKFFDSACTMGAYHPLLYEKNLVKHLNQGTDEDIY-LLGKATLPGFRTIHC
          .TD...Y.Q.FF.SACTMG..H.LLY...LVK.LN.GTDEDIY..LGKATLPGF...HC
Retrocopy ETDLGCYHQQFFNSACTMGTHHLLLY---LVKCLNKGTDEDIY<SLGKATLPGFWANHC

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	20.57 RPM
SRP007412_cerebellum	0.00 RPM	7.54 RPM
SRP007412_heart	0.00 RPM	11.92 RPM
SRP007412_kidney	0.00 RPM	46.90 RPM
SRP007412_liver	0.00 RPM	782.85 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3575 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3575 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3575 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010357	1 retrocopy	retro_btau_1767,
Canis familiaris	ENSCAFG00000013698	1 retrocopy	retro_cfam_2158,
Felis catus	ENSFCAG00000013886	1 retrocopy	retro_fcat_1983,
Macaca mulatta	ENSMMUG00000014905	1 retrocopy	retro_mmul_630,
Nomascus leucogenys	ENSNLEG00000006676	1 retrocopy	retro_nleu_2774,
Pongo abelii	ENSPPYG00000014388	1 retrocopy	retro_pabe_3575 ,