RetrogeneDB ID: retro_pabe_3490

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 9:82278002..82279014(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSPPYG00000001483
• Aliases: None
• Description: Nuclear transcription factor Y subunit gamma [Source:UniProtKB/Swiss-Prot;Acc:Q5RA23]

Sequence

>retro_pabe_3490
GAGGCGTTTGTCGAAATGTCCACAGAAGGAGGATTTGGTGGTACTAGCAGCAGTGATGCCCAGCAAAGCCTAAAGTCCTT
CTGGCCTCGGGTCATGGAAGAAATCTGGAATTTAGCAGTGAAAAATTTCGGAGTGCAGGAACTCCCACTGGCTCGTATTA
AGATTATGAAACTGGATGAAGATGTGAAGATGATCAGTGCAGAGGCCCCTGTGCTTTTTGCCAGGGCAGCCCAGATTTTT
ATCACAGAGTTGACTCTTCGAGCCTGGATTCACACAGAGGATAACAAGTGCTGGACTCTACAGAGAAATGATATCGCCAT
GGCAATTACAAAATGTGATCAATTTGATTTTCTCATCGATATTGTTCTAAGAGATGAGCTGAAACCTCCAAAGTGTCAGG
AGGAGGTGCTGCAGTCTGTAACTCCTGCTGAGCCAGTCCAGTACTATTTCAGGCTGGCTCAGCAGCCCACCGCCCTCCAA
ATCCAGGGGCAGCAGCAAGGCCAGACCACGGCCAGCTCCATGACCACCATCCAGCCTGGGCAGATCATCATCGCACAGCT
TCAGCAGGGCCAGACCACGCCCGTGACGACGCAGGTTGGAGAAGGTCAGCAGATGCCGATAGTGCAGGTCCAGCCACAGG
GTCAAGCCCAGTAGGCCCAGAGTGGTACTAGATGGACGGTGCAGGTGATGTAGCAGATCCTCACTAACACAGGAGAGATC
CAGCAGATCCCGGTGCAGCTGAAGGCTGGCCAGCTGCAGTGTATCCGCTTAGCCCAGTCTGTATCAGGCACCCAAGTTCT
GCAGGGGACAGATCCAGACACTTGCCACCAGTGCTCAACCGATTACACAGACAGAGGGTCCAGCAAAGACAGCAGTAGTT
CAGCCAGTTCACAGATGGACAGTAGCTCTACCAGATCCAGCAAGTATCCATACCTGCGGGCCAGGACCTGCCCAGCCCAT
GTTTATCCAGTCAACCAGCCCTCTGATGGGCAGGCCCCCCCAGGTGACTGGC

Alignment

ORF - retro_pabe_3490 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.92 %
• Parental protein coverage: 95.49 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EEVVEMSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEA
          E..VEMSTEGGFGGTSSSDAQQSL.SFWPRVMEEI.NL.VK.F.VQELPLARI.KIMKLDEDVKMISAEA
Retrocopy EAFVEMSTEGGFGGTSSSDAQQSLKSFWPRVMEEIWNLAVKNFGVQELPLARI-KIMKLDEDVKMISAEA

Parental  PVLFAKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEDVRQS
          PVLFA.AAQIFITELTLRAWIHTEDNK..TLQRNDIAMAITK.DQFDFLIDIV.RDELKPPK.QE.V.QS
Retrocopy PVLFARAAQIFITELTLRAWIHTEDNKCWTLQRNDIAMAITKCDQFDFLIDIVLRDELKPPKCQEEVLQS

Parental  VTPAEPVQYYFTLAQQPAAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQ
          VTPAEPVQYYF.LAQQP.A.Q.QGQQQGQ.T.SS.TTIQPGQIIIAQ.QQGQTTPVT.QVGEGQQ..IVQ
Retrocopy VTPAEPVQYYFRLAQQPTALQIQGQQQGQTTASSMTTIQPGQIIIAQLQQGQTTPVTTQVGEGQQMPIVQ

Parental  AQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQ-GQIQTLATNA
          .QPQGQAQ.AQSGT..T.QVM.QI.TNTGEIQQIPVQL.AGQLQ.IRLAQ.VSGTQV.Q.GQIQTLAT.A
Retrocopy VQPQGQAQ*AQSGTRWTVQVM*QILTNTGEIQQIPVQLKAGQLQCIRLAQSVSGTQVLQ>GQIQTLATSA

Parental  QQITQTE-VQQGQQQFSQFTDGQQLYQIQQVTMPAGQDL-AQPMFIQSANQPSDGQAPQVTG
          Q.ITQTE.VQQ.QQ.FSQFTDGQ.LYQIQQV..PAGQDL.AQPMFIQS...P..G..PQVTG
Retrocopy QPITQTE>VQQRQQ*FSQFTDGQ*LYQIQQVSIPAGQDL<AQPMFIQSTS-PLMGRPPQVTG

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	30.74 RPM
SRP007412_cerebellum	0.00 RPM	31.25 RPM
SRP007412_heart	0.00 RPM	13.67 RPM
SRP007412_kidney	0.00 RPM	29.20 RPM
SRP007412_liver	0.00 RPM	22.58 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3490 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3490 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3490 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4280
Pan troglodytes	retro_ptro_2903
Gorilla gorilla	retro_ggor_2865
Macaca mulatta	retro_mmul_1202

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 21 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,
Nomascus leucogenys	ENSNLEG00000012195	2 retrocopies	retro_nleu_2369, retro_nleu_2850,
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,
Pongo abelii	ENSPPYG00000012258	1 retrocopy	retro_pabe_2246,
Pan troglodytes	ENSPTRG00000000596	2 retrocopies	retro_ptro_2903, retro_ptro_3102,