RetrogeneDB ID: retro_pabe_3771

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:67590800..67591656(-)
• Located in intron of: ENSPPYG00000020432

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_3771
ATGCCAGCAGCAACTGTACATCATAGCCAAAGAATTTGTGAAGTTTGGGCTTGCAACGTGGATGAAGAGATGAAGAAAAT
TCGTCAAGTTATCCGAAAATATAATTACGTTGCTATGGACACCGAGTTTCCAGGTGTGGCTGCAAGACCCATTGGAGAAT
TCAGGAGCAATGCTGACTATCAATACCAACTATTGCGATGTAATGTAGACTTGTTAAAGATAATTCAGCTAGGACTGACA
TTTATAAATGAGCAAGGAGAATACCCTCCAGGAACTTCAACTTGGCAGTTTAATTTTAAATTTAATTTGACAGAGGACAT
GTATGCCCAGAACTCTATAGAGCTACTAACAACATCTGGTATCCAGTTTAAAAAACATGATGAGGAAGGAATTGAGACCC
AGTACTTTGCAAGAACTTCTTATGACTTCAGGAGTGGTCCTCTGTGAAGGGGTCAAATGGTTGTCATTTCACAGCAGTTA
CAACTTTGGCTATTTAATCAAAATCCTGACCAACTCTAACTTGCCTGAAGAAGAACTTGACTTCTTTGAGATCCTTCGAT
TGTTTTTACCTGTCATTTATGATGTGAAGTACCTCATGAAGAGCTGCAAACATCTCAAAGATGGATTACAGGAGGTGGCA
GAACAGTTAGAGCTGGCATAGATACGACCACCACATCAGGCAGGATCTAATTCATTCCTCACAGGAATGGCCTTTTTCAA
AATGAGAGGAATGTTCTTTGAAGATCATACTGATGATGCCAAATATTGTGGTCATTTGTATGGCCTTGGTTCTGGTTCAT
CCTATGTACAGAATGGCACAGGGAATGCATATGAAGAAGAAGCCAACAAGCAGTCA

Alignment

ORF - retro_pabe_3771 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.01 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPAATVDHSQRICEVWACNLDEEMKKIRQVIRKYNYVAMDTEFPGVVARPIGEFRSNADYQYQLLRCNVD
          MPAATV.HSQRICEVWACN.DEEMKKIRQVIRKYNYVAMDTEFPGV.ARPIGEFRSNADYQYQLLRCNVD
Retrocopy MPAATVHHSQRICEVWACNVDEEMKKIRQVIRKYNYVAMDTEFPGVAARPIGEFRSNADYQYQLLRCNVD

Parental  LLKIIQLGLTFMNEQGEYPPGTSTWQFNFKFNLTEDMYAQDSIELLTTSGIQFKKHEEEGIETQYFA-EL
          LLKIIQLGLTF.NEQGEYPPGTSTWQFNFKFNLTEDMYAQ.SIELLTTSGIQFKKH.EEGIETQYFA.EL
Retrocopy LLKIIQLGLTFINEQGEYPPGTSTWQFNFKFNLTEDMYAQNSIELLTTSGIQFKKHDEEGIETQYFA>EL

Parental  LMTSGVVLCEGVKWLSFHSGYDFGYLIKILTNSNLPEEELDFFEILRLFFPVIYDVKYLMKSCKNLKGGL
          LMTSGVVLCEGVKWLSFHS.Y.FGYLIKILTNSNLPEEELDFFEILRLF.PVIYDVKYLMKSCK.LK.GL
Retrocopy LMTSGVVLCEGVKWLSFHSSYNFGYLIKILTNSNLPEEELDFFEILRLFLPVIYDVKYLMKSCKHLKDGL

Parental  QEVAEQLELERIGPQHQAGSDSLLTGMAFFKMREMFFEDHIDDAKYCGHLYGLGSGSSYVQNGTGNAYEE
          QEVAEQLEL..I.P.HQAGS.S.LTGMAFFKMR.MFFEDH.DDAKYCGHLYGLGSGSSYVQNGTGNAYEE
Retrocopy QEVAEQLELA*IRPPHQAGSNSFLTGMAFFKMRGMFFEDHTDDAKYCGHLYGLGSGSSYVQNGTGNAYEE

Parental  EANKQS
          EANKQS
Retrocopy EANKQS

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_3771 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3771 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3771 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4851
Macaca mulatta	retro_mmul_2592

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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,