RetrogeneDB ID: retro_hsap_4280

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:89699075..89700066(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000224887
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSG00000066136
• Aliases: NFYC, CBF-C, CBFC, H1TF2A, HAP5, HSM, NF-YC
• Description: nuclear transcription factor Y, gamma [Source:HGNC Symbol;Acc:7806]

Sequence

>retro_hsap_4280
ATGTCCACAGAAGGAGGATTTGGTGGTACTAGCCGCAGTGATGCCCAGCAAAGCCTAAAGTCCTTCTGGCTTCGGGTCAT
GGAAGAAATCTGGAATTTAGCAGTGAAAGATTTCTGAATGCAGGAACTCCCACTGGCTCGTATTAAGAAGATTATGAAAC
TGGATGAAGATGTGAAGATGATCAGTGCAGAGGCCCCTGTGCTCTTTGCCAGGGCAGCCCAGATTTTTTATCACAGAGTT
GACTCTTCGAGCCTGGATTCACACAGAGGATAACAACTGCCGGACTTATGTCGCCATGGCAATTACGAAATTTGATCAAT
TGGATTTTCTCATCGATATTGTTCTAAGAGATGAACTGAAACCTCCAAAGTGTCAGGAGGAGGTGCTGCAGTCTGTAACT
CCTGCTGAGCCAGTCCAATACTATTTCACGCTGGCTCAGCAGCCCACCGCCCGTCCAAGTCCAGGGACAGCAGCAAGGCC
AGACCACCGCCAGCTCCATGACCACCATGCAGCCTGGGCAGATCATCATCGCACAGCTTCAGCAGGGCCAGACCACGCCC
GTGACGACGCAGGTTGGAGAAGGTCAGCAGGTGCAGATTGTCCAGGCCCAGCCACAGGGTCAAGCCCAGTAGGCCCAGAG
TGGTACTGGATGGACCGTGCAGGTGATGTAGCAGATCCTCACTAACACAGGAGAGATCCAGCAGATCCCGGTGCAGCTGA
AGGCTGGCCAGCTGCAGTGTATCCGCTTAGCCCAGTCTGTATCAGGCACCCACGTTCTGCAGGGACAGATCCAGACACTT
GCCACCAGCGCTCAACCGATTACACAGACAGAGGTCCAGCAAAGACAGCAGTAGTTCAGCCAGTTCACAGATGGACAGCA
GCTCTACCAGATCCAGCAAGTATCCATACCTGCGGGCCAGGACCTGCCCAGCCCATGTTTTTCCAGTCAGTCAACCAGCC
CTCTGATGGGCAGGCCCCCCGGGTGACTGGC

Alignment

ORF - retro_hsap_4280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.76 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFA
          MSTEGGFGGTS.SDAQQSL.SFW.RVMEEI.NL.VKDF..QELPLARIKKIMKLDEDVKMISAEAPVLFA
Retrocopy MSTEGGFGGTSRSDAQQSLKSFWLRVMEEIWNLAVKDF*MQELPLARIKKIMKLDEDVKMISAEAPVLFA

Parental  KAAQIF-ITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPA
          .AAQIF.ITELTLRAWIHTEDN..RT......AMAITKFDQ.DFLIDIV.RDELKPPK.QEEV.QSVTPA
Retrocopy RAAQIF>ITELTLRAWIHTEDNNCRTY----VAMAITKFDQLDFLIDIVLRDELKPPKCQEEVLQSVTPA

Parental  EPVQYYFTLAQQPTA-VQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQP
          EPVQYYFTLAQQPTA.VQVQGQQQGQ.T.SS.TT.QPGQIIIAQ.QQGQTTPVT.QVGEGQQVQIVQAQP
Retrocopy EPVQYYFTLAQQPTA>VQVQGQQQGQTTASSMTTMQPGQIIIAQLQQGQTTPVTTQVGEGQQVQIVQAQP

Parental  QGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQIT
          QGQAQ.AQSGTG.T.QVM.QI.TNTGEIQQIPVQL.AGQLQ.IRLAQ.VSGT.V.QGQIQTLAT.AQ.IT
Retrocopy QGQAQ*AQSGTGWTVQVM*QILTNTGEIQQIPVQLKAGQLQCIRLAQSVSGTHVLQGQIQTLATSAQPIT

Parental  QTEVQQGQQQFSQFTDGQQLYQIQQVTMPAGQDL-AQPMFIQSANQPSDGQAPQVTG
          QTEVQQ.QQ.FSQFTDGQQLYQIQQV..PAGQDL.AQPMF.QS.NQPSDGQAP.VTG
Retrocopy QTEVQQRQQ*FSQFTDGQQLYQIQQVSIPAGQDL<AQPMFFQSVNQPSDGQAPRVTG

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
bodymap2_adipose	0.00 RPM	31.29 RPM
bodymap2_adrenal	0.00 RPM	49.00 RPM
bodymap2_brain	0.00 RPM	23.63 RPM
bodymap2_breast	0.00 RPM	32.02 RPM
bodymap2_colon	0.00 RPM	28.19 RPM
bodymap2_heart	0.00 RPM	28.39 RPM
bodymap2_kidney	0.00 RPM	40.43 RPM
bodymap2_liver	0.00 RPM	22.12 RPM
bodymap2_lung	0.00 RPM	23.08 RPM
bodymap2_lymph_node	0.00 RPM	40.02 RPM
bodymap2_ovary	0.00 RPM	44.61 RPM
bodymap2_prostate	0.00 RPM	52.50 RPM
bodymap2_skeletal_muscle	0.00 RPM	57.38 RPM
bodymap2_testis	0.26 RPM	43.29 RPM
bodymap2_thyroid	0.00 RPM	49.53 RPM
bodymap2_white_blood_cells	0.00 RPM	54.42 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_4280 was not detected

EST

No EST(s) were mapped for retro_hsap_4280 retrocopy.

TSS

No TSS is located nearby retro_hsap_4280 retrocopy 5' end.

Lab

retro_hsap_4280 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_4280 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2903
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,
Homo sapiens	ENSG00000115350	1 retrocopy	retro_hsap_2765,
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,