RetrogeneDB ID: retro_pabe_863

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 12:76630405..76631596(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RTN4IP1
• Ensembl ID: ENSPPYG00000016882
• Aliases: None
• Description: reticulon 4 interacting protein 1 [Source:HGNC Symbol;Acc:18647]

Sequence

>retro_pabe_863
ATGGAATTTCTGAAGACTTGTGTACTTGGAAGAAATGCGTGTACTGCGGTTTGCTTCTGGAGAAGCAAAGTTGTCCAGAG
GCCTTCCATTAGAAGGATTAGTACTACCTCTCCAAGGAGCACTGTCATGCCTGCTTGGGTGATAGATAAGTATGGGAAGA
ACGAAGTGCTTCGATTGACTCAGAACATGATGTTACCTATCATATGCTATCCAAATGAAGTCATTGTAAAGTTCACCCTG
GCAGTGTAAATCCTATGGACGTCAATATGAGAAGTGGTTATGGAGCTACAGCTTTAAATATGAAGCGTAATCCTTTACAC
ATGAAAATCAAAGGAGAAGAATTTCCTCTGACTCTGGTTCGGGATGTCTCTGGCGTGATGATGGAATGTGGGCTTGACGT
GAAGTACTTCAAGCCTGGAGATGAGGTCTGGGCTGCAGTTCCTCCTTGGAAACAAGGCACTCTTTCAGAGTTTGTTGTAG
TCAGTGGAAACGAGGTCTCTCACAAACCCAAATCACTCACTCATCTATCAAGCTGCCTCTTCGCCATATGTGGCTCTCAC
AGCCTCATCTGCCATAAACAAAGTTGGTGGCCTGAATGACACGAATTGCACAGGAAGATGTGTTCAAATCTTAGGCGCTT
CAGGTGGAGTTGGTAGTTTTGCTATACAGGTAATAAAAGCATGGGATGCTCATGTGACAGCAGTTTGCGCTCAAGATGCC
AGTGAGCTTATAAAGAAGCTTGGGGCAGATGATGTAATTGATTACAAATTTGGAAGTGTGGAAGAGCAGTTGAAATCCTT
AAAACCGTTTGATTTCATCCTTGGTAATGTTGGCGGATCCACTGAAACATGGGCTCCAGATTTTCTCAAGAAATGGTCAG
GAGCCACCTATGTGACTTTGGTGAGTCCTTTCCTCCTGAACATGGACCGATTGGGCATAGCAGATGGCATGTTGCAGGCA
GGAGTCACTATAGGTTCGAAGGCATTAAAGCATTTCTGGAAAGGAGTCCATTATTGCTGGGCGTTTTTCATGGCCAGTGG
TCCACGTTTAGGTGACATTGCAGAACTGGTAGATGCGGGAAACATTGGACCAGTTATTGAACAAATCTTTCCTTTTTCTA
AAGTTCTAAGAAAAGCCTTCCTTAAGGTGGAAAGAGGACACACATGAGGAAAGACTGTAATTAATGTTGTT

Alignment

ORF - retro_pabe_863 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.97 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEFLKTCVLRRNACTAVCFWRSKVVPKPSVRRITTTSSRSTVMPAWVIDKYGKNEVLRFTQNMMLPIIHY
          MEFLKTCVL.RNACTAVCFWRSKVV..PS.RRI.TTS.RSTVMPAWVIDKYGKNEVLR.TQNMMLPII.Y
Retrocopy MEFLKTCVLGRNACTAVCFWRSKVVQRPSIRRISTTSPRSTVMPAWVIDKYGKNEVLRLTQNMMLPIICY

Parental  PNEVIVK-VHAASVNPIDVNMRSGYGATALNMKRDPLHMKIKGEEFPLTLGRDVSGVVMECGLDVKYFKP
          PNEVIVK.VH..SVNP.DVNMRSGYGATALNMKR.PLHMKIKGEEFPLTL.RDVSGV.MECGLDVKYFKP
Retrocopy PNEVIVK<VHPGSVNPMDVNMRSGYGATALNMKRNPLHMKIKGEEFPLTLVRDVSGVMMECGLDVKYFKP

Parental  GDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHT-QAASLPYVALTAWSAINKVGGLNDKNCTGKRV
          GDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTH..QAAS.PYVALTA.SAINKVGGLND.NCTG..V
Retrocopy GDEVWAAVPPWKQGTLSEFVVVSGNEVSHKPKSLTHL>QAASSPYVALTASSAINKVGGLNDTNCTGRCV

Parental  LILGASGGVGTFAIQVMKAWDAHVTAVCSQDASELVRKLGADDVIDYKSGSVEEQLKSLKPFDFILDNVG
          .ILGASGGVG.FAIQV.KAWDAHVTAVC.QDASEL..KLGADDVIDYK.GSVEEQLKSLKPFDFIL.NVG
Retrocopy QILGASGGVGSFAIQVIKAWDAHVTAVCAQDASELIKKLGADDVIDYKFGSVEEQLKSLKPFDFILGNVG

Parental  GSTETWAPDFLKKWSGATYVTLVTPFLLNMDRLGIADGMLQTGVTVGSKALKHFWKGVHYRWAFFMASGP
          GSTETWAPDFLKKWSGATYVTLV.PFLLNMDRLGIADGMLQ.GVT.GSKALKHFWKGVHY.WAFFMASGP
Retrocopy GSTETWAPDFLKKWSGATYVTLVSPFLLNMDRLGIADGMLQAGVTIGSKALKHFWKGVHYCWAFFMASGP

Parental  CLDDIAELVDAGKIRPVIEQTFPFSKV-PEAFLKVERGHARGKTVINVV
          .L.DIAELVDAG.I.PVIEQ.FPFSKV...AFLKVERGH..GKTVINVV
Retrocopy RLGDIAELVDAGNIGPVIEQIFPFSKVLRKAFLKVERGHT*GKTVINVV

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	3.76 RPM
SRP007412_cerebellum	0.00 RPM	4.50 RPM
SRP007412_heart	0.00 RPM	3.64 RPM
SRP007412_kidney	0.00 RPM	6.00 RPM
SRP007412_liver	0.00 RPM	2.88 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_863 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_863 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_863 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1030
Pan troglodytes	retro_ptro_705
Gorilla gorilla	retro_ggor_814

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000130347	1 retrocopy	retro_hsap_1030,
Gorilla gorilla	ENSGGOG00000008254	1 retrocopy	retro_ggor_814,
Nomascus leucogenys	ENSNLEG00000013349	1 retrocopy	retro_nleu_908,
Otolemur garnettii	ENSOGAG00000012703	1 retrocopy	retro_ogar_590,
Pongo abelii	ENSPPYG00000016882	1 retrocopy	retro_pabe_863 ,
Pan troglodytes	ENSPTRG00000018461	1 retrocopy	retro_ptro_705,