RetrogeneDB ID: retro_amel_1701

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194010.1:205551..206451(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NFYA
• Ensembl ID: ENSAMEG00000004435
• Aliases: None
• Description: nuclear transcription factor Y, alpha [Source:HGNC Symbol;Acc:7804]

Sequence

>retro_amel_1701
CAGGCTGGACATGTTCAGCAGCAGGTCCAGGGGCAGCCATTAATGGTACAGGGCAGTGGAGGCCAATCAATCCCATCAAC
TGGCCAACCCATCATGGTCCAAGCTGTCCCTGGTGCACAAGGTCAAACTGTCACATGAGTACCTGTGTGTGGGGTCCAGG
GTTTGCAGCAGATACAGTTGGTTCCACCTGGACAGATTCAGATCCGGGGGGGCAGGCCATGCAGGTGCAGGGCCATTGGG
GCCAGACCCGGCAGATCATCATCCTGCAGCCCCAGATGGCATTCACTCCTGGCCAGACCCAGACCCAGCAGCAGAATGCT
GTCCAGGGACAAGTGTCACAGATCGCTGCAGGGCAGACCACCATCTATTGGCCAGTTCATGCAGACGGCACCATTCTACA
GCACGTTACAGTCCCTGTTTCAGGACCACCACCATCCCAGCAGCCAGTTTGGCAGAAGCACAGATTGTTCTGACAGGAGC
TGACACCAACACAACCAGCAGTGGGCAAGGGGCTGTCACTGTGACAGTACCAGTGGCAGGCAATGTGGTCAGTTCAGGAG
GGATGGTCATGGTGGTGCCTGGTGCTGGCTCTGTACCTGCTATCCAAAGAATCCCTCTTCCTGGGGCAGAGATGCTCAGA
GAAGAGCCTCTCTATGTGAATGCCAAACATGTGGCCAAACATACACTAAAGAGGAGGCAAGCCTGGGCTCAACTAGAGGC
AGAAGGGAAGATTCCAAAGGAAAGAAGGAAATACCTGCATGAGTCTTGGCACCATCCAATCATGGCTCGGAAGCATGGCG
AAGGTGGATGGTTTTTCTTTCCAAAGAAAGAGGATAGTCCCCATATGCAGGATCCAAACAAAGCAGATGAAGAAGCAAGA
CACAGATCATTTGAGTGTCC

Alignment

ORF - retro_amel_1701 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.03 %
• Parental protein coverage: 86.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QVQTLQVVVQGQPLMVQVSGGQLITSTGQPIMVQAVPGGQGQTIMQVPVSGTQGLQQIQLVPPGQIQIQG
          Q....Q..VQGQPLMVQ.SGGQ.I.STGQPIMVQAVPG.QGQT...VPV.G.QGLQQIQLVPPGQIQI.G
Retrocopy QAGHVQQQVQGQPLMVQGSGGQSIPSTGQPIMVQAVPGAQGQTVT*VPVCGVQGLQQIQLVPPGQIQIRG

Parental  G-QAVQVQGQQGQTQQIIIQQPQTAVTAGQTQTQQQIAVQGQQVAQTAEGQTIVYQPVNADGTILQQVTV
          G.QA.QVQG..GQT.QIII.QPQ.A.T.GQTQTQQQ.AVQGQ.V.Q.A.GQT..Y.PV.ADGTILQ.VTV
Retrocopy G<QAMQVQGHWGQTRQIIILQPQMAFTPGQTQTQQQNAVQGQ-VSQIAAGQTTIYWPVHADGTILQHVTV

Parental  PVSG-MITIPAASLAGAQIVQTGANTNTTSSGQGTVTVTLPVAGNVVNSGGMVMMVPGAGSVPAIQRIPL
          PVSG...TIPAASLA.AQIV.TGA.TNTTSSGQG.VTVT.PVAGNVV.SGGMVM.VPGAGSVPAIQRIPL
Retrocopy PVSG<TTTIPAASLAEAQIVLTGADTNTTSSGQGAVTVTVPVAGNVVSSGGMVMVVPGAGSVPAIQRIPL

Parental  PGAEMLEEEPLYVNAKQYHR-ILKRRQARAKLEAEGKIPKERRKYLHESRHRHAMARKRGEGGRFFSPKE
          PGAEML.EEPLYVNAK......LKRRQA.A.LEAEGKIPKERRKYLHES.H...MARK.GEGG.FF.PK.
Retrocopy PGAEMLREEPLYVNAKHVAKHTLKRRQAWAQLEAEGKIPKERRKYLHESWHHPIMARKHGEGGWFFFPKK

Parental  KDSPHMQDPNQADEEA-MTQIIRVS
          .DSPHMQDPN.ADEEA..TQII.VS
Retrocopy EDSPHMQDPNKADEEA<KTQII*VS

Legend:

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

Expression

RNA-Seq

Ailuropoda melanoleuca was not studied using RNA-Seq expression data.

ChIP-Seq

Ailuropoda melanoleuca was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_amel_1701 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1701 was not experimentally validated.

Homology

Retrocopy orthology:

Ailuropoda melanoleuca 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.

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004435	1 retrocopy	retro_amel_1701 ,
Bos taurus	ENSBTAG00000009905	1 retrocopy	retro_btau_676,
Ictidomys tridecemlineatus	ENSSTOG00000023405	1 retrocopy	retro_itri_1410,