RetrogeneDB ID: retro_amel_485

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192470.1:1089872..1090842(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SF3A3
• Ensembl ID: ENSAMEG00000001262
• Aliases: None
• Description: splicing factor 3a, subunit 3, 60kDa [Source:HGNC Symbol;Acc:10767]

Sequence

>retro_amel_485
AAGAAGTTCATGCTCTGGTACCAGATCAATTCTGACCACTGCACATGGGCCATGCAAGAGAGGTATACGGAAGTCAGTAG
GAACCTGTGGGATTTGTATGATGATAAGAATGGATTAAGAAAGGAGGAACTCAATGCCATTTCAAGACCAAATGTATTAG
CTGAATTTTGTAGTAGACTCAGCAAATAAAATAATTTCACCAGAAATGAGATTTGTGTGCCAATGTCAGTGGAATTTGAG
GAGCTTCTGAAGGTTTGGGAGAATCCAAGTGAACAGGTTCTGAACTTGGTGGAATTCATAGATGAAGAGGGATATGGTCA
TTACCTTGCCATCCATGACTGTTAACCTCAAATACATTAACCTGAAGGCCTTGGGAGAAGCTGAATTATATCACATACTT
GTCTACCTTTGACCAGTTATTTGACATTTCTAAAGAAAGGAAGAATTTCAAAAATAAGAGATACCTGGAAATGCTGCTTG
ACTACCTTCAAGATTACACAGAACGAGTGAAGCTACTCCAAGATCAGAATGGACTTTTTAAGAAGATTCATAATGACTTT
GAGAGGTAGGAGAATAGTATCTTTCCTGGATGGCCAAAAGAGACAGGCGGAGCCCTGATCCATGCTGGAGCCCATCTTGA
CCTGTCTGCGTTCTCTTCTTGGGAGGAGTTGTCTTCCCTTGGTCTATACAGATTGCAATCTGCTCTCTTAGCTTTAGGCT
TGAAGTGTGGTGGGACCCTAGAAGAGTGAGTCCAGAGGCTATGCAGCACCAAGGAAATTTCCTGGATCACTTGACACCTC
CCTGCTTGCCAGAAATCCCAAGTCAAAGTCAAATGATACACTGAGAAGAACAAAGACATTGCCTTTCTAGAAGCCTACAT
CTGTGAATATGTAGAGATTCTTGGGGAAGAGCATCACCTCCTTCATGAAAATGGACATCACAAGGGGCCAGGACAGGGAA
AGAGTGAGAA

Alignment

ORF - retro_amel_485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.64 %
• Parental protein coverage: 65.67 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  KKSTLRDQINSDHRTRAMQDRYMEVSGNLRDLYDDKDGLRKEELNAISGPNEFAEFYNRLKQIKEFHRKH
          KK..L..QINSDH.T.AMQ.RY.EVS.NL.DLYDDK.GLRKEELNAIS.PN..AEF..RL.....F.R..
Retrocopy KKFMLWYQINSDHCTWAMQERYTEVSRNLWDLYDDKNGLRKEELNAISRPNVLAEFCSRLSK*NNFTR--

Parental  PNEICVPMSVEFEELLKARENPSEEAQNLVEFTDEEGYGRYLDLHDC-YLKYINLKAS-EKLDYITYLSI
          .NEICVPMSVEFEELLK..ENPSE...NLVEF.DEEGYG.YL..HDC..LKYINLKA..EKL.YITYLS.
Retrocopy -NEICVPMSVEFEELLKVWENPSEQVLNLVEFIDEEGYGHYLAIHDC>NLKYINLKAL>EKLNYITYLST

Parental  FDQLFDIPKERKNAEYKRYLEMLLEYLQDYTDRVKPLQDQNELFGKIQNEFEKKWENGTFPGWPKETSSA
          FDQLFDI.KERKN...KRYLEMLL.YLQDYT.RVK.LQDQN.LF.KI.N.FE...EN..FPGWPKET..A
Retrocopy FDQLFDISKERKNFKNKRYLEMLLDYLQDYTERVKLLQDQNGLFKKIHNDFER*-ENSIFPGWPKETGGA

Parental  LTHAGAHLDLSAFSSWEELASLGLDRLKSALLALGLKCGGTLEERAQRLFSTK-GKSLE-SLDTSLFAKN
          L.HAGAHLDLSAFSSWEEL.SLGL.RL.SALLALGLKCGGTLEE..QRL.STK.G..L..SLDTSL.A.N
Retrocopy LIHAGAHLDLSAFSSWEELSSLGLYRLQSALLALGLKCGGTLEE*VQRLCSTK<GNFLD<SLDTSLLARN

Parental  PKSKGTKRDTERNKDI-AFLEAQIYEYVEILGEQRHLTHENVQRK-QARTGEERE
          PKSK.......R.K...AFLEA.I.EYVEILGE..HL.HEN...K..ARTG.E.E
Retrocopy PKSK-SNDTLRRTKTL<AFLEAYICEYVEILGEEHHLLHENGHHK<GARTGKE*E

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_485 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_485 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001262	1 retrocopy	retro_amel_485 ,
Canis familiaris	ENSCAFG00000003222	1 retrocopy	retro_cfam_176,
Callithrix jacchus	ENSCJAG00000002176	1 retrocopy	retro_cjac_4109,
Cavia porcellus	ENSCPOG00000008660	1 retrocopy	retro_cpor_658,
Homo sapiens	ENSG00000183431	2 retrocopies	retro_hsap_2441, retro_hsap_937,
Macropus eugenii	ENSMEUG00000002534	3 retrocopies	retro_meug_1135, retro_meug_1346, retro_meug_642,
Macaca mulatta	ENSMMUG00000023199	1 retrocopy	retro_mmul_631,
Monodelphis domestica	ENSMODG00000017729	1 retrocopy	retro_mdom_269,
Nomascus leucogenys	ENSNLEG00000011720	1 retrocopy	retro_nleu_2775,
Pan troglodytes	ENSPTRG00000000559	2 retrocopies	retro_ptro_1411, retro_ptro_649,
Sorex araneus	ENSSARG00000014204	1 retrocopy	retro_sara_407,