RetrogeneDB ID: retro_amel_1874

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195035.1:3008..3897(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEST
• Ensembl ID: ENSAMEG00000005659
• Aliases: None
• Description: mesoderm specific transcript [Source:HGNC Symbol;Acc:7028]

Sequence

>retro_amel_1874
CTTTCCCTTGCTTTTCACTCATGGAAGTTGTCAGGCAAATTTTTCACCTACAAGGGACTATGCATCTTCTACCAAGACTC
TGTGGGTGTGGTTGGAATTCCTGAGATAGTTGTACTTTTAAATGGCTTTGCAGCATCCAGCTATGATTGGTACAAGATTT
GGAAAGGTCTGACCCTGAGGTTTCATGAGTGATTGCCCTTGATTTCTTGGGCTTTGGCTTCAGTGACAAACTGAGACCAG
ATTGCTATTCCATATTTGGGCAGGCCAGAATTGTGGAGGTGCTTTTGGGGTATCTGGGGCTTCAGAATTGCAAGACCAAC
TTTTTGTCTCATGATTATGGAGCTTCGTTGCTCAGGAGCCGCTCTTATATGTTCTAGTAGAATGGATCTGGTCAGCTTAC
CATAAAGAGTCTATGTCTGTCAAATGGATTTCCTGAGACTCCTTATCCTCTCTTTCTCCAAAACTTCTCAAAGATGGAGG
CATCCTGTCACCCATCCTCACCAAATTGAACTTCTTTGGATTCCCCCGAGGTCTCATCTCAGTCTTCAGCTGTACACCTG
ACCCTCTGAGAATGAGCTGTGGGACATGTAGTCAGGGATATGCAACAATGATGGGATAACTTCGTTATCAACAGTGTCTA
ACAATATATCAACCAGAGGAAGATGTTTAGAAAATGCTGGGTGGGAGCTCTTGCTTCCGTAAATATTCCCATTCTTTTAT
CTATGGGCCATTGGATCCTGTGAATCCGTATCCAGAGTTTTTGAAGCTGTACAGGAAAACACTGCCATAGTCCACAGTGT
CGATTCTGGATGACCACATTAGCCACTATCCACAGCTATAGGAAAATGTGGGGTTCTTGAAAGCATATATGGTCTTCATC
AGCAACTTT

Alignment

ORF - retro_amel_1874 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.24 %
• Parental protein coverage: 89.55 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LSPALHSWKSSGKFFTYKGLRIFYQDSVGVVGSPEIVVLLHGFPTSSYDWYKIWEGLTLRFHR-VIALDF
          LS.A.HSWK.SGKFFTYKGL.IFYQDSVGVVG.PEIVVLL.GF..SSYDWYKIW.GLTLRFH..VIALDF
Retrocopy LSLAFHSWKLSGKFFTYKGLCIFYQDSVGVVGIPEIVVLLNGFAASSYDWYKIWKGLTLRFHE<VIALDF

Parental  LGFGFSDKPRPHHYSIFEQASIVEALLRHLGLQNRRINLLSHDYGDIVAQELLYRFKQNRSGRLTIKSLC
          LGFGFSDK.RP..YSIF.QA.IVE.LL..LGLQN...N.LSHDYG........Y.F..N.SG.LTIKSLC
Retrocopy LGFGFSDKLRPDCYSIFGQARIVEVLLGYLGLQNCKTNFLSHDYGASLLRSRSYMF**NGSGQLTIKSLC

Parental  LSNGGIFPETHRPLLLQ-KLLKDGGMLSPILTRLMNFFVFSRGLTPVFG-PYTRPSESELWDMWAGIRNN
          LSNG..FPET..PL.LQ.KLLKDGG.LSPILT.L.NFF.F.RGL..VF...YT.PSE.ELWDM..GI.NN
Retrocopy LSNG--FPETPYPLFLQ<KLLKDGGILSPILTKL-NFFGFPRGLISVFS<LYT*PSENELWDM*SGICNN

Parental  DGNLVIDSLLQYINQR-KKFRRR-WVGALASVTIPI-HFIYGPLDPVNPYPEFLELYRKTLPRSTVSILD
          DG..........I..R..K..R..WVGALASV.IPI..FIYGPLDPVNPYPEFL.LYRKTLP.STVSILD
Retrocopy DGITSLSTVSNNISTR<RKMFRKCWVGALASVNIPI<SFIYGPLDPVNPYPEFLKLYRKTLP*STVSILD

Parental  DHISHYPQLEDPMGFLNAYMGFINSF
          DHISHYPQL....GFL.AYM.FI..F
Retrocopy DHISHYPQL*ENVGFLKAYMVFISNF

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_1874 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1874 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 15 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005659	2 retrocopies	retro_amel_1177, retro_amel_1874 ,
Callithrix jacchus	ENSCJAG00000010760	2 retrocopies	retro_cjac_1563, retro_cjac_3931,
Felis catus	ENSFCAG00000022984	5 retrocopies	retro_fcat_1067, retro_fcat_1645, retro_fcat_1693, retro_fcat_2004, retro_fcat_326,
Loxodonta africana	ENSLAFG00000006066	3 retrocopies	retro_lafr_578, retro_lafr_584, retro_lafr_748,
Macropus eugenii	ENSMEUG00000008227	1 retrocopy	retro_meug_885,
Microcebus murinus	ENSMICG00000006129	1 retrocopy	retro_mmur_1091,
Macaca mulatta	ENSMMUG00000009499	2 retrocopies	retro_mmul_1936, retro_mmul_94,
Nomascus leucogenys	ENSNLEG00000012841	3 retrocopies	retro_nleu_1065, retro_nleu_515, retro_nleu_790,
Otolemur garnettii	ENSOGAG00000009224	1 retrocopy	retro_ogar_3464,
Pongo abelii	ENSPPYG00000018006	4 retrocopies	retro_pabe_2337, retro_pabe_2510, retro_pabe_2511, retro_pabe_866,
Pan troglodytes	ENSPTRG00000019698	2 retrocopies	retro_ptro_1769, retro_ptro_2045,
Sorex araneus	ENSSARG00000000502	1 retrocopy	retro_sara_352,
Ictidomys tridecemlineatus	ENSSTOG00000020977	2 retrocopies	retro_itri_1210, retro_itri_1610,
Tupaia belangeri	ENSTBEG00000008404	2 retrocopies	retro_tbel_1480, retro_tbel_526,
Tursiops truncatus	ENSTTRG00000004934	4 retrocopies	retro_ttru_1026, retro_ttru_1115, retro_ttru_1133, retro_ttru_1907,