RetrogeneDB ID: retro_amel_1177

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193010.1:276547..277315(-)
• Located in intron of: ENSAMEG00000007701

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_1177
GTGCTTTTATATGAGTTTCCAACTTCCAGCTGTGATTGGTACAAGATTTGGGAAGGTCTGACCCTGGGGTTTTATTGAGT
GATTGTCCTTGATTTCTTGGGCTTTGGCTTCACTGACAAACCAAGACCACGTCACTTTTCCATATTTGAGCAGGCGAGCA
TTGTGGAGGCACTTTTGCAGCATCTGGGGCTCCAGAACCACAGGATCACCCTTTTGTCTCAAGATTACAGAGATATTATT
GCTCAAGAGGTGCTCTATAGGTTCAAGCAGGACTGATCTGGTCGGCTTACCGTGAAGAGTCTCTGGCTGTCAAATGGAGG
TATATTTCCTGAGACTCACCATCCTCTCCTTCTCCAAAAGCTTCTCAGAAATGGAGGCATGCTGTCACCCATCCACACAT
GATTGATGAACTTCTTTGTACTCTCCCAAAGTCTCACCCCAGTCTTTGGGCCATACATGCAATGCTCCGAGAGTGAGCTG
TGGGCCATGTGAGCAGTGATACCCAACAATGACAGAATTTAGTTACCATCAGTCTCTTACACTACATCAGCCAGAGAAGG
TTTAGAAGACGCCAGGTGGGAGCTCTTGCTTCTGTAACTGTTCCCATTCATTTTATCTATGGGCCATTGGATCCCATGAA
TCTCTACCCAGAGTTTTGGGATCTGTGTAGGAAAACCTTCCGATTCTGGATGACCACATTAGTCACTATCCACAGCTAGA
GGATCCCATGGGCTTCTTGAATACATATGTGACCTCATCAACTCCTTC

Alignment

ORF - retro_amel_1177 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.31 %
• Parental protein coverage: 78.51 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLLHGFPTSSYDWYKIWEGLTLRFHRVIALDFLGFGFSDKPRPHHYSIFEQASIVEALLRHLGLQNRRIN
          VLL..FPTSS.DWYKIWEGLTL.F..VI.LDFLGFGF.DKPRP.H.SIFEQASIVEALL.HLGLQN.RI.
Retrocopy VLLYEFPTSSCDWYKIWEGLTLGFY*VIVLDFLGFGFTDKPRPRHFSIFEQASIVEALLQHLGLQNHRIT

Parental  LLSHDYGDIVAQELLYRFKQNRSGRLTIKSLCLSNGGIFPETHRPLLLQKLLKDGGMLSPILTRLMNFFV
          LLS.DY.DI.AQE.LYRFKQ..SGRLT.KSL.LSNGGIFPETH.PLLLQKLL..GGMLSPI.T.LMNFFV
Retrocopy LLSQDYRDIIAQEVLYRFKQD*SGRLTVKSLWLSNGGIFPETHHPLLLQKLLRNGGMLSPIHT*LMNFFV

Parental  FSRGLTPVFGPYTRPSESELWDMWAGIRNNDG-NLVIDSLLQYINQRKKFRRRWVGALASVTIPIHFIYG
          .S..LTPVFGPY...SESELW.M.A.I.NND..NLV..SLL.YI.QR..FRRR.VGALASVT.PIHFIYG
Retrocopy LSQSLTPVFGPYMQCSESELWAM*AVIPNNDR<NLVTISLLHYISQRR-FRRRQVGALASVTVPIHFIYG

Parental  PLDPVNPYPEFLELYRKTLPRST-VSILDDHISHYPQLEDPMGFLNAYM-GFINSF
          ...P..P.....E.....L.R.T...ILDDHISHYPQLEDPMGFLN.Y....INSF
Retrocopy ---PLDPMNLYPEFW--DLCRKT<LPILDDHISHYPQLEDPMGFLNTYV<DLINSF

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_1177 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1177 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,