RetrogeneDB ID: retro_meug_1145

Retrocopy location

• Organism: Wallaby (Macropus eugenii)
• Coordinates: Scaffold30512:9287..10115(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYC
• Ensembl ID: ENSMEUG00000004480
• Aliases: None
• Description: nuclear transcription factor Y, gamma [Source:HGNC Symbol;Acc:7806]

Sequence

>retro_meug_1145
ATATCCACTGATGGAGAGTTTGGCAGTACCAGCAGCAGTGATGCTCAGCAGAGCCTACAGTCCTTTTGGCCTTGGTGTCA
TGGAAGAAATCCAAAATTTGACAGTGAAAGATTTCCGTGTGAAGGAACTTCCACTAGCTCATATAAAGAAGATCATGAAA
CTGGATGAAGATGTGAAGATGATAAGTGCTGAAGCCCCTGTGTTATTCTCCAAGGCTTCCCAGATATCCATCATTGAGTT
AACATTAGAGGCCTGTATCCACACAGAAGACAACAAACGATGGAGTCTCCAGAGAAATAACATTGCCATGGTGATTACAA
AATTTGACCAGTTCAACTTTCTTATCGATATTGTTCAAAGAGATGAACTAAAACCTACCAAGCATCAGGAGGAGGTGTGC
CAGTCTGTGACTCCTGCAGAGCCTGTCCAGTATACTTCACTGGCCCAGCAGCTGGTGATGGCCGTCCAGGTCCAGGGCCA
GCAGACTGGCCAGCAGACCACCTCCTGCACCACCACTATCCAGTCAGGACAGATCATCATTGCCCAGCCTCAGCAGGGCC
AGACCATCCCAGTGATGATGCCGGTTGGAGAATGCCAGCACATACAGATCATCCAGGCCCAACCCTAAGGCCAAACTCAA
CAAGCACCGAGCAGCATAGGACAGGCCATACAGGTGATGAAAGAGATCATCAATAACATGGGGGAAATCCAGCAAATTCC
CATTCAGTTAAATGTTGGCCAGCTGCAGTATATTTGCTTAGCCCAGACTGTATCAGACACTCAGTTTGCTCAGGGCAGAT
CCAGACTCTGGTGGCTAGTGCACAGCAG

Alignment

ORF - retro_meug_1145 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 87.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSTDGGFGSTSSSDAQQSLQSFWP-RVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLF
          .STDG.FGSTSSSDAQQSLQSFWP..VMEEI.NLTVKDFRV.ELPLA.IKKIMKLDEDVKMISAEAPVLF
Retrocopy ISTDGEFGSTSSSDAQQSLQSFWP>GVMEEIQNLTVKDFRVKELPLAHIKKIMKLDEDVKMISAEAPVLF

Parental  AKAAQIFITELTLRAWIHTEDNKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPA
          .KA.QI.I.ELTL.A.IHTEDNKR..LQRN.IAM.ITKFDQF.FLIDIV.RDELKP.K.QEEV.QSVTPA
Retrocopy SKASQISIIELTLEACIHTEDNKRWSLQRNNIAMVITKFDQFNFLIDIVQRDELKPTKHQEEVCQSVTPA

Parental  EPVQYYFTLAQQPTAAVQVQGQQTGQQTTTSTTTIQSGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQP
          EPVQ.Y..LAQQ...AVQVQGQQTGQQTT..TTTIQSGQIIIAQPQQGQT.PV.M.VGE.Q..QI.QAQP
Retrocopy EPVQ-YTSLAQQLVMAVQVQGQQTGQQTTSCTTTIQSGQIIIAQPQQGQTIPVMMPVGECQHIQIIQAQP

Parental  QGQTQQAPSSTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQ-GQIQTLAASAQQ
          .GQTQQAPSS.GQ..QVM..II.N.GEIQQIP.QLN.GQLQYI.LAQ.VS.TQ..Q.GQIQTL.ASAQQ
Retrocopy *GQTQQAPSSIGQAIQVMKEIINNMGEIQQIPIQLNVGQLQYICLAQTVSDTQFAQ<GQIQTLVASAQQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq

Macropus eugenii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_meug_1145 retrocopy.

TSS

Macropus eugenii was not studied using FANTOM5 data.

Lab

retro_meug_1145 was not experimentally validated.

Homology

Retrocopy orthology:

Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 18 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,