RetrogeneDB ID: retro_amel_1875

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195050.1:81549..82481(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEA3
• Ensembl ID: ENSAMEG00000009579
• Aliases: None
• Description: transcription elongation factor A (SII), 3 [Source:HGNC Symbol;Acc:11615]

Sequence

>retro_amel_1875
GCCAGGAAGAACATAGAAGGGGCCAGAAGAACATCTGAAGAAGCTGAACAGCTGTCAGATGTCCATCTGGCTACTCCAGA
CAACCAGGATTGGAGTTGCCATTAATGGGGTCTGCAAGTGCTGCTCAGACAAAAAGGTGGTGTGCTTGGCCAAAGTCCTC
GTCAAAAACCAAAGTCCTCGGCAGCTTTTGAACTCACCTGGGCCCCCCAAAGGAGAACGAGTAGAGGAAAGAAAAGGAAA
AAGGTCTGACTGTTCTGACTGGAAGCCAGAGGCAGGCCTTTCTCCACCAAGCCAAAATTAAGGTTAAGAGTCCAAAGACA
GGAGACACTCTGTGGACTCCAAGTCTCCAGCCATCTTCTTTCCAAAAAGACCATTGATAGAAAGATCAAACAGCAGCAAA
TCAAAAGCAGAGACTCCCAAAACACCCAGTAGCCCCTCAACCCCCTTTGCCCCCTCCATCTTCCTCCTGGCGCCCTGCTA
TCTCACAGGGAACTCTGTATGGGACAAGTGTATGGAGATGCTCTCAGCAGCCTCAAAGGCCAATGATGGTTACAAGGACT
ATAGAGTCACTGAGATAAGATGGCTTCAGTAATCGAAGATAATATCTATGAGGAGCTCAAAAGCATGGACATGAAGTACT
GGAACTTGGTACACAGCTGAATCAGAAACCTCAAGGACCCAGGAACCCCAGCCTGAGGAGGAATGTGCTCAGTGGGACCA
TCTCTGCTGGGCTCATTGCCAAGATGACGGCAGAGGAAATGGCCTGTGATGAGCTGAGGGAATTGGGGAATGCCATGATC
TAGGGGGTTACCCATCAGCACCAGATAACCAAGGCTGGTGGCACCACCACTGACTTCTTCCAGTACAGCAAATGCAAGAA
GAACTGCAGCAATAACCAGGTGCAGTCATGCAGTGCTGATAAGCCCATGACT

Alignment

ORF - retro_amel_1875 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.31 %
• Parental protein coverage: 94.59 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ARSREEGAL-DLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNW--KRLSDSPGPP
          AR...EGA....LKKLNSCQMSI.LLQTTRIGVA.NGV.K.CSDK.VV.LAKVL.KN.....L..SPGPP
Retrocopy ARKNIEGAR>EHLKKLNSCQMSIWLLQTTRIGVAINGVCKCCSDKKVVCLAKVLVKNQSPRQLLNSPGPP

Parental  KGEKGEERDKAKKEKGLDCSDWKAETGLSPPRKKRGEEPKDRRDSVGSKSSASSSPKRPSMERSNSSTSK
          KG....ER....K.K..DCSDWK.E.GLSPP....G.E.KDRR.SV.SKS.A...PKRP..ERSNSS.SK
Retrocopy KG----ERVEERKGKRSDCSDWKPEAGLSPPSQN*G*ESKDRRHSVDSKSPAIFFPKRPLIERSNSSKSK

Parental  AESPKTPGSPLTPTFAPSVCLLAPCYLTGDSVRDKCVEMLSAALKAEDDYKDYGV-NCDKMASEIEDHIL
          AE.PKTP.SP.TP.FAPS..LLAPCYLTG.SV.DKC.EMLSAA.KA.D.YKDY.V...DKMAS.IED.I.
Retrocopy AETPKTPSSPSTP-FAPSIFLLAPCYLTGNSVWDKCMEMLSAASKANDGYKDYRV<H*DKMASVIEDNIY

Parental  EELKSTDMKYRNRVRSRISNLKD-PRNPSLRRNVLSGTISAGLIAKMTAEEMASDELRELRNAMTQEAIR
          EELKS.DMKY.N.V.S.I.NLKD.PRNPSLRRNVLSGTISAGLIAKMTAEEMA.DELREL.NAM......
Retrocopy EELKSMDMKYWNLVHS*IRNLKD<PRNPSLRRNVLSGTISAGLIAKMTAEEMACDELRELGNAMI*GVTH

Parental  EHQMAKTGGTTTDLFQCSKCKKKNCTYNQVQTRSADEPMT
          .HQ..K.GGTTTD.FQ.SKC.KKNC..NQVQ..SAD.PMT
Retrocopy QHQITKAGGTTTDFFQYSKC-KKNCSNNQVQSCSADKPMT

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_1875 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1875 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009579	1 retrocopy	retro_amel_1875 ,
Felis catus	ENSFCAG00000011648	1 retrocopy	retro_fcat_467,