RetrogeneDB ID: retro_amel_1392

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193312.1:116859..119157(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSDE1
• Ensembl ID: ENSAMEG00000017129
• Aliases: None
• Description: None

Sequence

>retro_amel_1392
ATGAGCTTTGATCCAAACCTTCTCCATAACAATGGACACAATGGGTACCCTAACGGTACTTCAGCAGTACTGTGTGAAAC
AGGGGTTATTGAAAAACTGCTAACCTCTTACTGATTTATTCAGCGTTCAGAACGTCAAGCTAGATTTTTCTTCCACTGTT
CTCAGTATAATGGCAACTTGCAGGACTTAAAAGTGGGAGATGATGTTAAATTTGAAGTATTATCTGACCGGCGGACTGGG
AAACCCGTTGCTGTTAAACTGGTGAAGATAAAACCAGAAATCCTCCCTGAAGAAAGAATGAATGGACAAGAAGTGTTTTA
TCTGACTTACACCCCAGAAGATGTCGAAGGGAATGTTCAGCTGGAAACTGGAGATAAAATAAACTTTGTAATTGATAACA
ATAAACATACTGGTGCTGTCAGGGCTCGTAACATTATGCTGTTGAAAAAGAAACAAGCCCGCTGTCAGGGAGTAGTTTGT
GCCATGAAGGAGGCGTGTGGCTTTATTGAAAGAGGTGATATCGTAAAAGAGATATTCTTTCACTATAGTGAATTTAAGGG
TGACTTAGAAACCTTACAGCCTGGAGATGACGTGGAATTCACAATCAAGGACAGAAATGGTAAAGAAGTTGCAACAGATG
TCAGACTATTGCCTCAAGGAACAGTCATTTTTGAAGGTACCAGCATTGAACATTTTGAAGGAACTGTAACCAAAGTAATC
CCAAAAGTACCCAGTAAAAACCAGAATGACCCATTGCCAGGACGCATCAAAGTTGATTTTGTGATTCCTAAAGAACTTCC
CTTTGGAGACAAAGATACAAAATCCAAGGTGACCCTGCTGGAAGGCGACCACGTTAGGTTTAATATTTCAACAGACAGAC
GTGACAAATTAGAACAAGCAACCAACCTAGAAGTTCTATCAAATACATTTCAGGTCACTAATGAAGCCAGAGAAATGGGT
GTAAGAGCTGCCATGAGAGATGGTTTTGGTTTCATCAAGTGTGTGGATCGTGATGCTCGTATGTTCTTCCACTTCAGTGA
AATTCTGGATGGGAACCAGCTGCATATTGCAGATGAAGTAGCGTTTACTGTGGTTCCTGATATGCTCTCTGCCCAAAGAA
ATCATGCTATTAGCATTAAAAAGCTTCCCAAGGGCACGGTTTCATTCCACTCCCATTCAGATCATCGTTTTCTGGGCACT
GTAGAAAAAGAAGCCACTTTCTCCAATCCTAAAACCACTAGCCCAAATAAAGGCAAAGAAAAGGAGGCTGAAGATGGTGT
TATTGCTTGTGATGATTGTGGGGTGAAATTGACTATTGCTTTTCAAGCCAAGGATGTGGAAGGATCTACTTCTCCTCAAA
TAGGAGATAAGGGTGAATTTAGTATTAGTGACAAACAGAGGCCTGGACAACAGATTGCAACTTGTGTGTGACTTTTAGGT
CGTAATTCCAACTCCAAGAAGCTCTTGGGTTATGTGGCAACTGTGAAGGATAATTTTGGATTTATTGAAACAGCCAATCA
TGATAAGGAAATCTTTTTCCATTACAGTGAGTTCTCTGGTGATGTTGATAGCTTGGAACTAGGGGACATGGTCGAGTACA
GCTTGTCCAAAGGCAAAGGCAACAAAGTCAGTGCAGAAAAAAATGAACAAAACACACTCAGTGAATGGCATTACTGAGGA
AGCTGATCCCACCATCTACTCTGGGAAAGTCATTCGCCCCTTGAGGAGTGTTGATCCAACACAGACTGAGTACCAAGGAA
TGATTGAGATTATGGAGGAAGGGGATATGAAAGGTGAGGTCTATCCATTTGGCATAGTTGGGATGGCCAACAAAGGGGAT
TGCCTGCAGAAAGGGGAGAGTGTCAAGTTCCAATTGTGTGTCTTAGGCCAAAATGCACAGACTATGGTCAACATCACACC
CCTGCGTAGGGCCACAGTGGAGTGTGTGAAGGATCAGTTTGGCTTCATTAACTATGAAGTAGGAGATAGCAAGAAGCTCT
TTCCCATGTGAAAGAAGTTCAGGATGGCATTGAGCTACAGGCTGGAGATGAGGTGGAGTTCTCAGTGATTCTTAATCAGC
GCACTGGCAAGTGCAGCACTTGTAATGTTTGGTGAGTCTGCGAGGGCCCCAAGGCTGTTGCGGCTCCACGACCTGATAGG
TTGGTCAATCGCTTGAAGAACATCACCCTGGATGATGCCAGTACTCCTCGCCTAATGGTTCTTCATCAGCCAAGGGGACC
AGATAACTCAATGGGATTTGGTGCGGAAAGAAAGATCCGTCAAGCTGGTATCATTGAC

Alignment

ORF - retro_amel_1392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.23 %
• Parental protein coverage: 94.22 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFDPNLLHNNGHNGYPNGTSAALRETGVIEKLLTSYGFIQCSERQARLFFHCSQYNGNLQDLKVGDDVE
          MSFDPNLLHNNGHNGYPNGTSA.L.ETGVIEKLLTSY.FIQ.SERQAR.FFHCSQYNGNLQDLKVGDDV.
Retrocopy MSFDPNLLHNNGHNGYPNGTSAVLCETGVIEKLLTSY*FIQRSERQARFFFHCSQYNGNLQDLKVGDDVK

Parental  FEVSSDRRTGKPIAVKLVKIKPEILPEERMNGQEVFYLTYTPEDVEGNVQLETGDKINFVIDNNKHTGAV
          FEV.SDRRTGKP.AVKLVKIKPEILPEERMNGQEVFYLTYTPEDVEGNVQLETGDKINFVIDNNKHTGAV
Retrocopy FEVLSDRRTGKPVAVKLVKIKPEILPEERMNGQEVFYLTYTPEDVEGNVQLETGDKINFVIDNNKHTGAV

Parental  SARNIMLLKKKQARCQGVVCAMKEAFGFIERGDIVKEIFFHYSEFKGDLETLQPGDDVEFTIKDRNGKEV
          .ARNIMLLKKKQARCQGVVCAMKEA.GFIERGDIVKEIFFHYSEFKGDLETLQPGDDVEFTIKDRNGKEV
Retrocopy RARNIMLLKKKQARCQGVVCAMKEACGFIERGDIVKEIFFHYSEFKGDLETLQPGDDVEFTIKDRNGKEV

Parental  ATDVRLLPQGTVIFEGTSIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLL
          ATDVRLLPQGTVIFEGTSIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLL
Retrocopy ATDVRLLPQGTVIFEGTSIEHFEGTVTKVIPKVPSKNQNDPLPGRIKVDFVIPKELPFGDKDTKSKVTLL

Parental  EGDHVRFNISTDRRDKLERATNIEVLSNTFQFTNEAREMGVIAAMRDGFGFIKCVDRDARMFFHFSEILD
          EGDHVRFNISTDRRDKLE.ATN.EVLSNTFQ.TNEAREMGV.AAMRDGFGFIKCVDRDARMFFHFSEILD
Retrocopy EGDHVRFNISTDRRDKLEQATNLEVLSNTFQVTNEAREMGVRAAMRDGFGFIKCVDRDARMFFHFSEILD

Parental  GNQLHIADEVEFTVVPDMLSAQRNHAISIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKGKE
          GNQLHIADEV.FTVVPDMLSAQRNHAISIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKGKE
Retrocopy GNQLHIADEVAFTVVPDMLSAQRNHAISIKKLPKGTVSFHSHSDHRFLGTVEKEATFSNPKTTSPNKGKE

Parental  KEAEDGVIAYDDCGVKLTIAFQAKDVEGSTSPQIGDKVEFSISDKQRPGQQIATCV-LLGRNSNSKKLLG
          KEAEDGVIA.DDCGVKLTIAFQAKDVEGSTSPQIGDK.EFSISDKQRPGQQIATCV.LLGRNSNSKKLLG
Retrocopy KEAEDGVIACDDCGVKLTIAFQAKDVEGSTSPQIGDKGEFSISDKQRPGQQIATCV*LLGRNSNSKKLLG

Parental  YVATVKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAE-KVNKTHSVNGITE
          YVATVKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAE.K.NKTHSVNGITE
Retrocopy YVATVKDNFGFIETANHDKEIFFHYSEFSGDVDSLELGDMVEYSLSKGKGNKVSAE>KMNKTHSVNGITE

Parental  EADPTIYSGKVIRPLRSVDPTQTEYQGMIEIVEEGDMKGEVYPFGIVGMANKGDCLQKGESVKFQLCVLG
          EADPTIYSGKVIRPLRSVDPTQTEYQGMIEI.EEGDMKGEVYPFGIVGMANKGDCLQKGESVKFQLCVLG
Retrocopy EADPTIYSGKVIRPLRSVDPTQTEYQGMIEIMEEGDMKGEVYPFGIVGMANKGDCLQKGESVKFQLCVLG

Parental  QNAQTMAYNITPLRRATVECVKDQFGFINYEVGDSKKLF-FHVKEVQDGVELQAGDEVEFSVILNQRTGK
          QNAQTM..NITPLRRATVECVKDQFGFINYEVGDSKKLF..HVKEVQDG.ELQAGDEVEFSVILNQRTGK
Retrocopy QNAQTMV-NITPLRRATVECVKDQFGFINYEVGDSKKLF<SHVKEVQDGIELQAGDEVEFSVILNQRTGK

Parental  CSACNVWRVCEGPKAVAAPRPDRLVNRLKNITLDDASTPRLMVLHQPRGPDNSMGFGAERKIRQAGVID
          CS.CNVW.VCEGPKAVAAPRPDRLVNRLKNITLDDASTPRLMVLHQPRGPDNSMGFGAERKIRQAG.ID
Retrocopy CSTCNVW*VCEGPKAVAAPRPDRLVNRLKNITLDDASTPRLMVLHQPRGPDNSMGFGAERKIRQAGIID

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_1392 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1392 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017129	1 retrocopy	retro_amel_1392 ,
Cavia porcellus	ENSCPOG00000000538	2 retrocopies	retro_cpor_1402, retro_cpor_513,
Myotis lucifugus	ENSMLUG00000005681	1 retrocopy	retro_mluc_1011,
Mus musculus	ENSMUSG00000068823	1 retrocopy	retro_mmus_1757,
Rattus norvegicus	ENSRNOG00000030302	1 retrocopy	retro_rnor_1429,