RetrogeneDB ID: retro_pabe_2449

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:86831468..86832412(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AMT
• Ensembl ID: ENSPPYG00000013871
• Aliases: None
• Description: aminomethyltransferase [Source:HGNC Symbol;Acc:473]

Sequence

>retro_pabe_2449
CAGACCGAGATACGTGGTGGTGACCTGGTGAAGCTGATGCAGGGTCTAGTGGTTGGAGACATTGCAGAGCTAAGGCCAAA
CCAGAGGACACTGTTGCTGCTTACTCATGAGGCTAGAGGCACCTTAGATGACTTGATTGTGATCAGTACTTCTGAGGGGC
ACCTATATGTGATGTTCAACACTGGCTGCTGGGAAAAAGACTTGGCCTTCATGCAGGACAAGATCAGAGAACTTCAGAGG
CAGGGCAGGGATGTGGGCCTGGAGGTGGTGAATACTGCCCTGCTAGCCCTGCAAGGGCCCCCTGTGGCCCAGGTGCTACA
GGCTGGGGCAGCAGCTGACCTGAGGAAACTGCCTTCATGACTAGTGCTGTGATGGAGGTGTTTGACGTGTCTGGCCGCCA
CCTTACCCACTGTGGCTGCACAGGAGAGAATGGCGTGGACACCTTGGTGCCAGCAGCGGGGGCAGTTCACCCAGCATCAG
CTCTTCTGGAAAACCCAGAGGCGAAGCTGGCAGTGCTGGCAGTGCTGGCAGCTTGCGCCTGGAGGCAGGCCTCTGGCTGT
ACAGGAGTGACACTGATGAACACACTACCCCTGTGGAGGGCAGCCTCAGTTGGACATTGGGGAAGTGCCACTGAGCTGCT
CTCGACTTCCCTGGAGCCAAGGTCATTGTTCCCCAGCTGAAGGGAAAGTGCAGTGGAGGTGTGTGGGGTTGATGTGTGAG
GGGGCCCTGATGCAGGCACACAGTCCCACCTGAGCATCGAGGGTCCATGATTCGTACTGTGACCAGTGGCTGTCCCTTGC
CCTACCTGAAGAAGAATGTGGCAATGGGTTACATGCCCTGCCAGTAGTCAGCCAGGGGCAATGCTGCTGGTAGAGGTGCG
GCGGAAGCAGCAGATGGGCGCAGTCAGCAAGATGCCCTTTGCGCCCATGAACTGCTCTACCCTC

Alignment

ORF - retro_pabe_2449 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.66 %
• Parental protein coverage: 78.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  QTKILGSDRVKLMESLVVGDIAELRPNQGTLSLFTNEAGGILDDLIVTSTSEGHLYVVSNAGCWEKDLAL
          QT.I.G.D.VKLM..LVVGDIAELRPNQ.TL.L.T.EA.G.LDDLIV.STSEGHLYV..N.GCWEKDLA.
Retrocopy QTEIRGGDLVKLMQGLVVGDIAELRPNQRTLLLLTHEARGTLDDLIVISTSEGHLYVMFNTGCWEKDLAF

Parental  MQDKVRELQNQGRDVGLEVLDNALLALQGPTAAQVLQAGVADDLRKLP-FMTSAVMEVFGVSGCRVTRCG
          MQDK.RELQ.QGRDVGLEV...ALLALQGP..AQVLQAG.A.DLRKLP.FMTSAVMEVF.VSG...T.CG
Retrocopy MQDKIRELQRQGRDVGLEVVNTALLALQGPPVAQVLQAGAAADLRKLP<FMTSAVMEVFDVSGRHLTHCG

Parental  YTGEDGVEISVPVAGAVHLATALLKN-PEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLG
          .TGE.GV...VP.AGAVH.A.ALL.N.P............LRLEAGL.LY..D.DEHTTPVEGSLSWTLG
Retrocopy CTGENGVDTLVPAAGAVHPASALLEN<PRGEXXXXXXXXXLRLEAGLWLYRSDTDEHTTPVEGSLSWTLG

Parental  KRRRAAMDFPGAKVIVPQLK-GKVQRRRVGLMCEGAPMRAHSPI-LNME-GTKIGTVTSGCPSPSLKKNV
          K...AA.DFPGAKVIVPQLK.GKVQ.R.VGLMCEGA.M.AHSP..L..E.G..I.TVTSGCP.P.LKKNV
Retrocopy KCH*AALDFPGAKVIVPQLK<GKVQWRCVGLMCEGALMQAHSPT<LSIE<GSMIRTVTSGCPLPYLKKNV

Parental  AMGYVPCEYSRPGT-MLLVEVRRKQQMAVVSKMPFVPTNYYTL
          AMGY.PC..S..G...L....R...QM..VSKMPF.P.N..TL
Retrocopy AMGYMPCQ*SARGN>LLVEVRRKQ-QMGAVSKMPFAPMNCSTL

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	27.31 RPM
SRP007412_cerebellum	0.00 RPM	39.52 RPM
SRP007412_heart	0.00 RPM	24.59 RPM
SRP007412_kidney	0.03 RPM	56.75 RPM
SRP007412_liver	0.03 RPM	31.43 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2449 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2449 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2449 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2953

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011489	1 retrocopy	retro_cfam_1035,
Callithrix jacchus	ENSCJAG00000003962	1 retrocopy	retro_cjac_1895,
Homo sapiens	ENSG00000145020	1 retrocopy	retro_hsap_2953,
Monodelphis domestica	ENSMODG00000012973	1 retrocopy	retro_mdom_1809,
Pongo abelii	ENSPPYG00000013871	1 retrocopy	retro_pabe_2449 ,
Rattus norvegicus	ENSRNOG00000050214	1 retrocopy	retro_rnor_1397,