RetrogeneDB ID: retro_pabe_428

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 1:112597965..112598567(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CNOT7
• Ensembl ID: ENSPPYG00000018385
• Aliases: None
• Description: CCR4-NOT transcription complex, subunit 7 [Source:HGNC Symbol;Acc:14101]

Sequence

>retro_pabe_428
CCAGCAGCAACTGTAGCTCATAGCCCAAGAATTTGTGAAGTTTGGGCTTGCAACTTGGATGAAGAGATGAAGAAAATTCG
TCAAGTTATCCGAAAATATCATTACGTTGCTATGGACACCGAGTGTCCAGATGTGGTTGCAAGACCTATTACAGAATTCA
GGAGCAATCCTGACTATCAGTATCAACTATTGCGGTGTAATGTAGACTTGTTAAAGATAATTAGCTAGGACTGACATTTA
TGAATGAGCAAGGTGAATACCCTCCAGGAACTTCAACTTGGCAGCTTAATTTTAAATTTAATTTGACGGAGGACATGCAT
GCCCAGCACTCTATAGAGCTACTAACAACATCTGATATCCAGTATAAAAAACATTAGGAGGAAGGAATTGAGACCCAGTA
CTTTGCTGAACTTATGACTTCGGGAGTGCTCCTCTGTGAAGGGGTCAACTGGTTGTCATTTCATAGCAGTTATGACTTTG
GCTATTTAATTAAAATCTTGACCAACTCTAACTTGCCTGAAGAAGAACTTGACTTCTTTGAGATCCTTCGACTGTTTTTT
CATGTCATTTATGCTGTGAAGTAGCTCATGAAGAGCTGCAAA

Alignment

ORF - retro_pabe_428 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.16 %
• Parental protein coverage: 70.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVDL
          PAATV.HS.RICEVWACNLDEEMKKIRQVIRKY.YVAMDTE.P.VVARPI.EFRSN.DYQYQLLRCNVDL
Retrocopy PAATVAHSPRICEVWACNLDEEMKKIRQVIRKYHYVAMDTECPDVVARPITEFRSNPDYQYQLLRCNVDL

Parental  LKIIQ-LGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFAELL
          LKII..LGLTFMNEQGEYPPGTSTWQ.NFKFNLTEDM.AQ.SIELLTTS.IQ.KKH.EEGIETQYFAE.L
Retrocopy LKIIS<LGLTFMNEQGEYPPGTSTWQLNFKFNLTEDMHAQHSIELLTTSDIQYKKH*EEGIETQYFAE-L

Parental  MTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCK
          MTSGV.LCEGV.WLSFHS.YDFGYLIKILTNSNLPEEELDFFEILRLFF.VIY.VK.LMKSCK
Retrocopy MTSGVLLCEGVNWLSFHSSYDFGYLIKILTNSNLPEEELDFFEILRLFFHVIYAVK*LMKSCK

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	12.99 RPM
SRP007412_cerebellum	0.00 RPM	14.11 RPM
SRP007412_heart	0.00 RPM	6.68 RPM
SRP007412_kidney	0.00 RPM	12.36 RPM
SRP007412_liver	0.00 RPM	9.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_428 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_428 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_428 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000677	4 retrocopies	retro_chof_1431, retro_chof_1581, retro_chof_822, retro_chof_963,
Callithrix jacchus	ENSCJAG00000011795	1 retrocopy	retro_cjac_720,
Felis catus	ENSFCAG00000000591	1 retrocopy	retro_fcat_1889,
Homo sapiens	ENSG00000198791	2 retrocopies	retro_hsap_211, retro_hsap_4851,
Macaca mulatta	ENSMMUG00000001873	1 retrocopy	retro_mmul_2592,
Mustela putorius furo	ENSMPUG00000017972	1 retrocopy	retro_mputfur_1596,
Nomascus leucogenys	ENSNLEG00000002489	2 retrocopies	retro_nleu_1860, retro_nleu_2373,
Oryctolagus cuniculus	ENSOCUG00000014589	1 retrocopy	retro_ocun_118,
Otolemur garnettii	ENSOGAG00000006324	2 retrocopies	retro_ogar_1883, retro_ogar_505,
Pongo abelii	ENSPPYG00000018385	2 retrocopies	retro_pabe_3771, retro_pabe_428 ,
Sarcophilus harrisii	ENSSHAG00000011828	2 retrocopies	retro_shar_103, retro_shar_631,
Ictidomys tridecemlineatus	ENSSTOG00000009175	2 retrocopies	retro_itri_1729, retro_itri_1730,