RetrogeneDB ID: retro_ptro_2903

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:85915478..85916304(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSPTRG00000000596
• Aliases: None
• Description: None

Sequence

>retro_ptro_2903
ATGTCCACAGAAGGAGGATTTGGTGGTACTAGCCGCAGTGATGCCCAGCAAAGCCTAAAGTCCTTCTGGCTTCGGGTCAT
GGAAGAAATCTGGAATTTAGCAGTGAAAGATTTCTGAATGCAGGAACTCCCACTGGCTCGTATTAAGAAGATTATGAAAC
TGGATGAAGATGCGAAGATGATCAGTGCAGAGGCCCCTGTGCTCTTTGCCAGGGCAGCCCAGATTTTTTATCACAGAGTT
GACTCTTCGAGCCTGGATTCACACAGAGGATAACAAGTGCCGGACTCTACAGAGAAATGATGTCGCCATGGCAATTACGA
AATTTGATCAATTTGATTTTCTCATCGATATTGTTCTAAGAGATGAACTGAAACCTCCAAAGTGTCAGGAGGAGGTGCTG
CAGTCTGTAACTCCTGCTGAGCCAGTCCAATACTATTTCACGCTGGCTCAGCAGCCCACCGCCGTCCAAGTCCAGGGACA
GCAGCAAGGCCAGACCACCGCCAGCTCCATGACCACCATGCAGCCTGGGCAGATCATCATCGCACAGCTTCAGCAGGGCC
AGACCACGCCCGTGACGACGCAGGTTGGAGAAGGTCAGCAGGTGCAGATTGTCCAGGCCCAGCCACAGGGTCAAGCCCAG
TAGGCCCAGAGTGGTACTGGATGGACCGTGCAGGTGATGTAGCAGATCCTCACTAATGCAGGAGAGATCCAGCAGATCCC
GGTGCAGCTGAAGGCTGGCCAGCTGCAGTGTATCTGCTTAGCCCAGTCTGTATCAGGCACCCAAGTTCTGCAGGGACAGA
TCCAGACACTTGCCACCAGCACTCAA

Alignment

ORF - retro_ptro_2903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 77.68 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFA
          MSTEGGFGGTS.SDAQQSL.SFW.RVMEEI.NL.VKDF..QELPLARIKKIMKLDED.KMISAEAPVLFA
Retrocopy MSTEGGFGGTSRSDAQQSLKSFWLRVMEEIWNLAVKDF*MQELPLARIKKIMKLDEDAKMISAEAPVLFA

Parental  KAAQIF-ITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPA
          .AAQIF.ITELTLRAWIHTEDNK.RTLQRND.AMAITKFDQFDFLIDIV.RDELKPPK.QEEV.QSVTPA
Retrocopy RAAQIF>ITELTLRAWIHTEDNKCRTLQRNDVAMAITKFDQFDFLIDIVLRDELKPPKCQEEVLQSVTPA

Parental  EPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQPQ
          EPVQYYFTLAQQPTAVQVQGQQQGQ.T.SS.TT.QPGQIIIAQ.QQGQTTPVT.QVGEGQQVQIVQAQPQ
Retrocopy EPVQYYFTLAQQPTAVQVQGQQQGQTTASSMTTMQPGQIIIAQLQQGQTTPVTTQVGEGQQVQIVQAQPQ

Parental  GQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQ
          GQAQ.AQSGTG.T.QVM.QI.TN.GEIQQIPVQL.AGQLQ.I.LAQ.VSGTQV.QGQIQTLAT..Q
Retrocopy GQAQ*AQSGTGWTVQVM*QILTNAGEIQQIPVQLKAGQLQCICLAQSVSGTQVLQGQIQTLATSTQ

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	47.39 RPM
SRP007412_cerebellum	0.04 RPM	53.34 RPM
SRP007412_heart	0.03 RPM	28.50 RPM
SRP007412_kidney	0.05 RPM	51.36 RPM
SRP007412_liver	0.03 RPM	32.64 RPM
SRP007412_testis	0.00 RPM	36.15 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2903 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2903 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2903 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4280
Gorilla gorilla	retro_ggor_2865
Pongo abelii	retro_pabe_3490
Macaca mulatta	retro_mmul_1202

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000012591	1 retrocopy	retro_acar_33,
Bos taurus	ENSBTAG00000021943	1 retrocopy	retro_btau_1338,
Callithrix jacchus	ENSCJAG00000002987	1 retrocopy	retro_cjac_4050,
Homo sapiens	ENSG00000066136	2 retrocopies	retro_hsap_4280, retro_hsap_4668,
Gorilla gorilla	ENSGGOG00000007360	2 retrocopies	retro_ggor_2865, retro_ggor_2896,
Macropus eugenii	ENSMEUG00000004480	1 retrocopy	retro_meug_1145,
Macaca mulatta	ENSMMUG00000014970	2 retrocopies	retro_mmul_1202, retro_mmul_2485,
Mus musculus	ENSMUSG00000032897	1 retrocopy	retro_mmus_844,
Otolemur garnettii	ENSOGAG00000012614	2 retrocopies	retro_ogar_2147, retro_ogar_411,
Pongo abelii	ENSPPYG00000001483	3 retrocopies	retro_pabe_1712, retro_pabe_3490, retro_pabe_3628,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903 , retro_ptro_3102,
Pan troglodytes	ENSPTRG00000012105	1 retrocopy	retro_ptro_1872,