RetrogeneDB ID: retro_amel_1537

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193570.1:56861..58089(-)
• Located in intron of: ENSAMEG00000014180

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNH1
• Ensembl ID: ENSAMEG00000010466
• Aliases: None
• Description: ribonuclease/angiogenin inhibitor 1 [Source:HGNC Symbol;Acc:10074]

Sequence

>retro_amel_1537
ACCAAGAATCTGGACATTCAGTGTAAGCAGTTGAGTGATGCTAGTTGGAGAGAGTTCCCGCCTCTGATCCAACTGTTTGA
GGTGGTCAGGCTGGATGACAGGGGCCTCAAAGAGCTGTGTTGAAAGGATGTCACCTGTGCTCTCTGGGCCAACCTCTCCC
TGACTGAGGTAGCCTTTGCACCAAAGAGCTGGGTGATGCTGGTAGGCACCTGGTGCTCCAGGGCCTGTAGAGCCCCACCT
GCAAGATATAGAAGCTCAGCCTCCAGAACTGCTGCCTGATGGAGGCTGGCTGTGGAGTCCTGCCCTGCGTGCTGCACTTG
GTGCCCGTCCTGCATGAACTGCACTTCAGAGACAATTCGTTGGCAGATGCAGGCCTGCAGCTGTTCTCCAAAGATCTCCT
GGACTCCCAGTGCCACCTTGAGACACTTCAGCTGGAGTACTGCAACCTGACAGCTGCCAGTTGTGAGCCCCTAGCTGTGG
TGTTCAAAGGCCAAGCCACACTCCAAGGAGCTCATGGTGACCAACAATGACATCTGTGAGGGGGCATCTGAGTGCTGTAC
CAGGGCCTGGTAGACTCTGCCTTTCAGTTGGAGATGCTCAAGTTGGAGAACTGTGGCTTCACGTTGGCCAATGGTAAGGA
TCTGTGTAGTATTGTGACCTCCAAGGTGCTGGACCTGGGTGACAAGCTGGGTGACCTGGGTATTGTCGAGATGTGCCCCA
AAATGCTACACCCCAGCTCCTGACTCAGGGCCCTGTGGCTCTGGGACTGTGACATCACCACTAGGGGCTGCAGAGACCTG
TGCCACGTCCATAGGGCCAAGGAGAGCCTGAAGAATTGAGCCTGGTGGGCAATGTGCTGGGGGACAAGGGTGCCTGGCTA
CATGTGAGAGCCTGTGGGAACCTGGCTGCCAGATGCAGTATCCATGGGTGAAGTCCTGCAGCTTACGGCCATCTGCTGCC
ACCATTTCAGCATGACATAGACCCAAAATAGTATCTCATGGAGTTGCAGATGAGCAACAACAAGCTAGGGGATTCTGGAG
TCCGGGAGCTCTGCCGAGGTCTGGGCCATCCTGGCACCCCACTGTGAGCGCCCTGGCTGGGGGAATGCGACTGATGGACA
GTGGCTGTAGCAGCCTGGCCTTGCTCCTGCTGGCCAACCCCAGCCTGCACAAGCAGGAATTCAGGCAACAACTACATGTG
CTCTGAAATAGCATGGCATCTACTGGAT

Alignment

ORF - retro_amel_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.12 %
• Parental protein coverage: 91.03 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  TMSLDIQCQQLSDARWTELLPLLQQSEVVRLDDCGLTEMRCKDISSALQANPSLTEL-SLCTNELGDAGV
          T..LDIQC.QLSDA.W.E..PL.Q..EVVRLDD.GL.E...KD...AL.AN.SLTE..SLCT.ELGDAG.
Retrocopy TKNLDIQCKQLSDASWREFPPLIQLFEVVRLDDRGLKELC*KDVTCALWANLSLTEV<SLCTKELGDAGR

Parental  HLVLQGLQSPTCKIRKLSLQNCCLTKTGCGVLPDMLRSMPTLRELYLNDNPLGDAGLQLLCSGLLDPQCH
          HLVLQGL.SPTCKI.KLSLQNCCL...GCGVLP..L...P.L.EL...DN.L.DAGLQL....LLD.QCH
Retrocopy HLVLQGL*SPTCKI*KLSLQNCCLMEAGCGVLPCVLHLVPVLHELHFRDNSLADAGLQLFSKDLLDSQCH

Parental  LEKLQVEYCNLTAASCESLASALR-AKRHFKELAVSNNELGEA-GVRVLCRGLVDSACQLEVLKLENCGL
          LE.LQ.EYCNLTAASCE.LA.....AK.H.KEL.V.NN...E..G..VL..GLVDSA.QLE.LKLENCG.
Retrocopy LETLQLEYCNLTAASCEPLAVVFK>AKPHSKELMVTNNDICEG<GI*VLYQGLVDSAFQLEMLKLENCGF

Parental  TSASCEDLCGVVASKPSLQELDLGDNKLGDQGIATLCPRLLHPSCQIRVLWLWDCDITTAGCRDLCRVLR
          T.A...DLC..V.S......LDLGD.KLGD.GI...CP..LHPS...R.LWLWDCDITT.GCRDLC.V.R
Retrocopy TLANGKDLCSIVTS----KVLDLGD-KLGDLGIVEMCPKMLHPSS*LRALWLWDCDITTRGCRDLCHVHR

Parental  AKESLK-EMSLAGNALGDEGARL-LCESLLEPACQLQSLWVKSCS-FTAASCQHFSSMLTRNTC-LVELQ
          AKESLK.E.SL.GN.LGD.GA.L..CESL.EP.CQ.Q..WVKSCS..TA..C.HFS...T.N...L.ELQ
Retrocopy AKESLK<ELSLVGNVLGDKGAWL<TCESLWEPGCQMQYPWVKSCS<LTAICCHHFSMT*TQNSI<LMELQ

Parental  LSNNKLGDCGVQQLCQGLSQPGAALQVLWLGDCD-VAHSGCASLASVLLVNRSLRELDL-SNNCMGEEGI
          .SNNKLGD.GV..LC.GL..PG..L...WLG.CD....SGC.SLA..LL.N.SL.......NN.M..E..
Retrocopy MSNNKLGDSGVRELCRGLGHPGTPL*APWLGECD<LMDSGCSSLALLLLANPSLHKQEF>GNNYMCSEIA

Parental  LRLME
          ..L..
Retrocopy WHLLD

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_1537 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1537 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010466	1 retrocopy	retro_amel_1537 ,
Felis catus	ENSFCAG00000007585	1 retrocopy	retro_fcat_1347,
Mus musculus	ENSMUSG00000038650	2 retrocopies	retro_mmus_1727, retro_mmus_1778,