RetrogeneDB ID: retro_amel_1763

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL194233.1:184528..186046(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF1
• Ensembl ID: ENSAMEG00000017828
• Aliases: None
• Description: splicing factor 1 [Source:HGNC Symbol;Acc:12950]

Sequence

>retro_amel_1763
CTGGACTTCCCAAGTATGAAGTGGAAGAGGAGCCACTGGAAACAAGATACAATGAAACAGAAGATGGCAAATCCAGGAAT
GCCTACATTTTTCTCCCCTGGACTTACTCGGGAACAAGAAAGAGCTTATTTAGTGCAACTGCAGATAGAAGACCTGATTC
ATAAACTGTGCACAGGAGACCTGAACATCCCCCCACAACCCTGAGGACAGGTCCCCTTCCACTGAGCCCATCTACAATAT
CAAGGGGAAGAGGCTTAACACTCACCATGTTCCGCACCGGCAAAATTCCTGAAGAGGAGCAGCCCAACGTCATCACGGGG
ATGGCTGCCTTCAGCCCTGATTTTAAGCCTCCTGCAGATTACAAACCTCCAACAACCTGTGTAGCGATAAAATAATGATT
CCACAAGATGCATATCCAGAAATCAACTTCGTGGGGCTGCTGATTGGGCCCCGAGGGGACACCTTGAAGAACATAGAGGA
GGAGTGTAATACCAAGATTATAATCTGGGGAAAAGGGTCTGCCAAAGAAGCGAAAGCTGGGCGCGAAGACGGCCAGATGT
TGCCTGGAGAAGGTGAGCCATTTCATGCCCTAGTTACCGCCAACACCATGGAGAATGTGAAGAAAGCCATGGAACGGATA
AGAAACCTCATGAAACAGGGTATTGAGACCCCTGAGGACCAAAATGATCTATGGAAGATGCAGCTTCTATAGCTGGCTTG
CTTGAATGGGACCCTTCAGGAAGACGATAACAGGATCATAGGACCCTGGCAAAGCTCAGAGACCTGCAGCATTACCAATA
CCACAGTGCGTACCAAGGATGCCCACAGTGCTTCTGATTGCAAATTCCCAAGGCCTGCTGACCCCCAGTCAGCTCAGGAT
AAAGCACGGATGGATGAAGAATATTTGTCCCTCATGGCTGAACCAGGTGAAGCGCCCATGGGCCCCATCTCTGGCCCACC
ACCACGCCCCTGGCCAGCGCACCTGGGCCTACTGTCCCTGCCAACCACCCACCTCCACTGTCTCATGTCCACCTCCCAAG
CTGCCCACCCTGAATGATGAATTCTGGCACTTCGGAGATTTGGCCCTACCATGGCGTGCGCAGAGGTGGTCCTGGTGGGC
CTGGAGGTGGCCCCCACAGCTTCCCACACCCATTACCCAGCCTGACAGGTGGGCATGCTGGACGTCCCATGCAGCATAAC
CCTAATGGACCCCCACTCCCTTGGAGGCAACCACCACCAACGCAGATGAACCAGGGCTCCCACCCACCTGGGCTCCACCG
CTTTCCTCCAGTGGATCAGTACCTGGGAAGTATGACTGTGGGCTCTGGGGTCAATTGTCCACATCGAGGAAAAGTTACGA
TGCCAACCACCACCTATGGGCATGATGCGGCCCTGTCTCCCAGTGGACAGCCCCCGCCCCCTCCCTCTTCTCCCATGGCA
GCAGCAGCAGCAGCCTCCACCACACCCCTTCTGCTCAGCAGCAGTATGTCTTCCAGTACCCCCTTGCCATGGCAGCAA

Alignment

ORF - retro_amel_1763 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.52 %
• Parental protein coverage: 80.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LDFPSKKRKRSRWNQDTMEQKTVIPGMPTVIPPGLTREQERAYIVQLQIEDLTRKLRTGDLGIPP-NPED
          LDFPS.K.KRS.W.QDTM.QK...PGMPT...PGLTREQERAY.VQLQIEDL..KL.TGDL.IPP.NPED
Retrocopy LDFPSMKWKRSHWKQDTMKQKMANPGMPTFFSPGLTREQERAYLVQLQIEDLIHKLCTGDLNIPP>NPED

Parental  RSPSPEPIYNSEGKRLNTRE-FRTRKKLEEERHNLITEMVALNPDFKPPADYKPPATRV-SDKVMIPQDE
          RSPS.EPIYN..GKRLNT...FRT.K..EEE..N.IT.M.A..PDFKPPADYKPP.T.V.SDK.MIPQD.
Retrocopy RSPSTEPIYNIKGKRLNTHH>FRTGKIPEEEQPNVITGMAAFSPDFKPPADYKPPTTCV<SDKIMIPQDA

Parental  YPEINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVK
          YPEINFVGLLIGPRG.TLKNIE.ECN.KI.I.GKGS.KE.K.GR.DGQMLPGE.EP.HALVTANTMENVK
Retrocopy YPEINFVGLLIGPRGDTLKNIEEECNTKIIIWGKGSAKEAKAGREDGQMLPGEGEPFHALVTANTMENVK

Parental  KAVEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAG
          KA.E.IRN..KQGIETPEDQNDL.KMQL..LA.LNGTL.EDDNRI..PWQSSET.SITNTTV.TK.....
Retrocopy KAMERIRNLMKQGIETPEDQNDLWKMQLL*LACLNGTLQEDDNRIIGPWQSSETCSITNTTVRTK---DA

Parental  HIASDCKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGP-AATPLASAPRPAAPANNPPP
          H.ASDCKF.RP.DPQSAQDKARMD.EYLSLMAE.GEAP.....G..SGP...TPLASAP.P..PAN.PPP
Retrocopy HSASDCKFPRPADPQSAQDKARMDEEYLSLMAEPGEAPM----GPISGP<TTTPLASAPGPTVPANHPPP

Parental  PSLMSTTQSRPPWMNSGPSESRPYHGMHGGGPGGPGGGPHSFPHPLPSLTGGHGGHPMQHNPNGPPPPWM
          .S........P..MNSG.SE..PYHG...GGPGGPGGGPHSFPHPLPSLTGGH.G.PMQHNPNGPP.PW.
Retrocopy LSHVHLPSCPP*MMNSGTSEIWPYHGVRRGGPGGPGGGPHSFPHPLPSLTGGHAGRPMQHNPNGPPLPWR

Parental  QPPPPPMNQGPHPPGHHGPPPMDQYLGSTPVGSGVYRLHQGKGMMP-PPPMGMMPPPPPPPSGQPPPPPS
          QPPP..MNQG.HPPG.H..PP.DQYLGS..VGSGV...H.GK..MP.PPPMGMM...P..P...P.P...
Retrocopy QPPPTQMNQGSHPPGLHRFPPVDQYLGSMTVGSGVNCPHRGKVTMP>PPPMGMMR--PCLPVDSPRPL--

Parental  GPLPPWQQQQQQPP-PPPPPSSSMASSTPLPWQQ
          .PL.PWQQQQQ.PP..P...SSSM.SSTPLPWQQ
Retrocopy -PLLPWQQQQQPPP<TPLLLSSSMSSSTPLPWQQ

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_1763 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1763 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017828	1 retrocopy	retro_amel_1763 ,
Canis familiaris	ENSCAFG00000014239	1 retrocopy	retro_cfam_2148,
Callithrix jacchus	ENSCJAG00000002780	1 retrocopy	retro_cjac_1930,
Ictidomys tridecemlineatus	ENSSTOG00000009790	1 retrocopy	retro_itri_698,