RetrogeneDB ID: retro_pabe_3822

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:151309954..151311012(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAB1
• Ensembl ID: ENSPPYG00000013025
• Aliases: None
• Description: NGFI-A-binding protein 1 [Source:RefSeq peptide;Acc:NP_001127431]

Sequence

>retro_pabe_3822
TGTGTGCAGAGCTTGGGACAGGGGAAGTCAGATGTGGTCGGGAGCCTAGCACTGCAGAGTGCTGGTGAGTCCAGACTCTG
GCAAGGCCACCATGCCACCAAGAGCGAGCACAGCCTCTCCCCAGCAGACCTGGGCTCCCACACGTCCCCAAAGGAGAGCA
GCGAGGCACTGGATGCTGCTGCTGTGCTCTCTGTGGCAGAGTGTGTGGAGCGGATGGCCCCCACACTGCCGAAAAGTGAC
TTGAACAAAGTGAAAGAGCTGCTAAAAGTCAACAAGAAGTTGGCCAAAATGATTGGTCACATCTTTGAGATGAACGATAA
TTATCCACACAAAGAGGAGGAAATTTGGAAATACAGTGAATATATGGCAGATTTGACTCAAAGAGGAAGGATGGAAAACA
TCTCATTCTTCATGAGCTCACTGTTAATGAAGCGGCTGCTCAACTCTGTGTGAAGGATAATGCTCTGATGACAAGAAGAG
ATGAGCTTTTTGCCTTGGCTAGGCAGATTTCTCGAGAAGTCACCTATAAATATACTTACAGAACCACCAAGTCAAAATGT
GAAGAAAGAGGTGAATTATCCTTGTAGAGGATTAAAGTGGAGGATGGGTTTCCAGATTTCCAGGATTCTGTGCAAACGCT
CTTCCAGCTGGCTAGAGCTAAGAGTGAAGAACTCGCAGCTCTTAGTTCACAGCAGCCTGAAAAGGTGATGGCAAAGCAGA
TGGAGTTCCTTTGCAACCAAGCTGGCTATGAGAGACTGCAGCATGCCGAGACAAGGCTGTCTGCAGGGCTTTACAGGCGG
AGCTCAGAAGAGCACAGTCCTAAAGGCCTGACTTCCGATAACCCAGATGGACAAGGAGAAAGACCTTTGAATCTCCGAAT
GCCTAATTTACAGAACAGACAACCCCATAATTTTGTGGTGGATGGGGAGCTGAGCAGACTTTATCCCAGTGAGGCAAAGT
CCCACTCATCAGGGAGCCTTGGGATTTTAAAAGACCACCCTCACTCAGCTTTTACCTTAGAAAAGAAAGTCATCAAAACA
GGCCCTGAAGATTCAAGA

Alignment

ORF - retro_pabe_3822 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.81 %
• Parental protein coverage: 72.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CVQSLGQGKSDVVGSLALQSVGESRLWQGHHATESEHSLSPADLGSPASPKESSEALDAAAALSVAECVE
          CVQSLGQGKSDVVGSLALQS.GESRLWQGHHAT.SEHSLSPADLGS..SPKESSEALDAAA.LSVAECVE
Retrocopy CVQSLGQGKSDVVGSLALQSAGESRLWQGHHATKSEHSLSPADLGSHTSPKESSEALDAAAVLSVAECVE

Parental  RMAPTLPKSDLNEVKELLKTNKKLAKMIGHIFEMNDDDPHKEEEIRKYSA-IYGRFDSKRKDGKHLTLHE
          RMAPTLPKSDLN.VKELLK.NKKLAKMIGHIFEMND..PHKEEEI.KYS..IYGRFDSKRKDGKHL.LHE
Retrocopy RMAPTLPKSDLNKVKELLKVNKKLAKMIGHIFEMNDNYPHKEEEIWKYSE<IYGRFDSKRKDGKHLILHE

Parental  LTVNEAAAQLCVKDNALLTRRDELFALARQISREVTYKYTYRTTKSKCGERDELSPKRIKVEDGFPDFQE
          LTVNEAAAQLCVKDNAL.TRRDELFALARQISREVTYKYTYRTTKSKC.ER.ELS..RIKVEDGFPDFQ.
Retrocopy LTVNEAAAQLCVKDNALMTRRDELFALARQISREVTYKYTYRTTKSKCEERGELSL*RIKVEDGFPDFQD

Parental  SVQTLFQQARAKSEELAALSSQQPEKVMAKQMEFLCNQAGYERLQHAERRLSAGLYRQSSEEHSPNGLTS
          SVQTLFQ.ARAKSEELAALSSQQPEKVMAKQMEFLCNQAGYERLQHAE.RLSAGLYR.SSEEHSP.GLTS
Retrocopy SVQTLFQLARAKSEELAALSSQQPEKVMAKQMEFLCNQAGYERLQHAETRLSAGLYRRSSEEHSPKGLTS

Parental  DNSDGQGERPLNLRMPNLQNRQPHHF-VDGELSRLYPSEAKSHSSESLGILKDYPHSAFTLEKKVIKTEP
          DN.DGQGERPLNLRMPNLQNRQPH.F.VDGELSRLYPSEAKSHSS.SLGILKD.PHSAFTLEKKVIKT.P
Retrocopy DNPDGQGERPLNLRMPNLQNRQPHNFVVDGELSRLYPSEAKSHSSGSLGILKDHPHSAFTLEKKVIKTGP

Parental  EDSR
          EDSR
Retrocopy EDSR

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	12.22 RPM
SRP007412_cerebellum	0.12 RPM	59.83 RPM
SRP007412_heart	0.00 RPM	12.04 RPM
SRP007412_kidney	0.00 RPM	21.58 RPM
SRP007412_liver	0.00 RPM	11.11 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3822 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3822 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3822 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Gorilla gorilla	retro_ggor_3068

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010241	1 retrocopy	retro_chof_2490,
Callithrix jacchus	ENSCJAG00000005748	1 retrocopy	retro_cjac_4224,
Gorilla gorilla	ENSGGOG00000013842	1 retrocopy	retro_ggor_3068,
Microcebus murinus	ENSMICG00000007306	2 retrocopies	retro_mmur_1155, retro_mmur_1211,
Nomascus leucogenys	ENSNLEG00000006665	1 retrocopy	retro_nleu_2288,
Pongo abelii	ENSPPYG00000013025	1 retrocopy	retro_pabe_3822 ,
Ictidomys tridecemlineatus	ENSSTOG00000000098	1 retrocopy	retro_itri_1621,
Tupaia belangeri	ENSTBEG00000011954	1 retrocopy	retro_tbel_3626,