RetrogeneDB ID: retro_amel_905

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192729.1:163715..164220(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBPMS
• Ensembl ID: ENSAMEG00000001522
• Aliases: None
• Description: RNA binding protein with multiple splicing [Source:HGNC Symbol;Acc:19097]

Sequence

>retro_amel_905
CAAACACCTGTCCAGACCCCATTTGTCAGTGGTGTCCCCCTGGGTATCCCACCTCGGGAGCTCTAGCTGCTTTTCCGACC
ATTGAAGGACTACGGGGTTCTCTTATAAAACCCACATCTAGGCAGTCCATAGGGTTTGTCAGTTTTGACAGCTGCTTAGA
AGCAGAAGTTGCAAAGAATGCTTTGAATGGCATTCACTTTGATCCTGGAATCCCTCAAACACTAGGGCTAGAGTTGGCTA
AGGCAACCACGAAGATGGCCGAGAACAAGCTAGCGGAGACTCCGAGGCCCGGTACTCCCCTGCCCAGCTCTGTACTTCGC
TCAGTTCATTGCCAGGGAGCCATCGGAGCCTACCGTGCCTGCACTTCACCCAGGAGCCCCGAAGTGTGGGCCCCGTACCC
TCTGTAGCCAGCAGAGTTCGCCCTTGCTCTCCCTGCCCCACTTTCCCCTGTCGCGCCTCACTGCGTGCCCAGATGCACGG
GCTCCCTCCCTCCGAGGCGACTCCT

Alignment

ORF - retro_amel_905 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.32 %
• Parental protein coverage: 76.71 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  QLEVRTLFVSGLPLDIKPRELYLLFRPFKGY-EGSLIKLTSKQPVGFVSFDSRSEAEAAKNALNGIRFDP
          Q..V.T.FVSG.PL.I.PREL.LLFRP.K.Y..GSLIK.TS.Q..GFVSFDS..EAE.AKNALNGI.FDP
Retrocopy QTPVQTPFVSGVPLGIPPREL*LLFRPLKDY<RGSLIKPTSRQSIGFVSFDSCLEAEVAKNALNGIHFDP

Parental  EIPQTLRLEFAKANTKMAKNKLVGTPNPST-PLPNTV-PQFIAREPYELTVPALYPS-SPEVWAPYPLYP
          .IPQTL.LE.AKA.TKMA.NKL..TP.P.T.P.P.....QFIAREP.E.TVPAL.P..SPEVWAPYPL.P
Retrocopy GIPQTLGLELAKATTKMAENKLAETPRPGT>PCPALYFAQFIAREPSEPTVPALHPG<SPEVWAPYPL*P

Parental  AELAPALPP-PAFTYPASLHAQCFSPEAKPNTP
          AE.A.ALP..P.F...ASL.AQ.........TP
Retrocopy AEFALALPA<PTFPCRASLRAQMHGLPPSEATP

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_905 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_905 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001522	1 retrocopy	retro_amel_905 ,
Bos taurus	ENSBTAG00000033727	1 retrocopy	retro_btau_1555,
Callithrix jacchus	ENSCJAG00000012366	1 retrocopy	retro_cjac_2705,
Tarsius syrichta	ENSTSYG00000013982	2 retrocopies	retro_tsyr_1171, retro_tsyr_1397,