RetrogeneDB ID: retro_amel_1891

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195290.1:34280..35019(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSAMEG00000004417
• Aliases: None
• Description: CAP, adenylate cyclase-associated protein 1 (yeast) [Source:HGNC Symbol;Acc:20040]

Sequence

>retro_amel_1891
TTGAGTGTATGGACAGAGCTACAGGCTTACATTAAGGACTTCTGTCCCACTGGACTGGCCTGAACCAAAACAGGGCCTGT
GGCAGAACAGAGTGGATTGCCATCTGGGCCTTCTGCTGGATCGGGTCCCCCGCCTCCCCCACCAGACTGGCCCTCCTCAC
CAAGTCCCCACCATTCAGGCTCGGATGAGTCTACTTCCCACTCGCACTGTTCACACAGATTAATCCGGGGGAGAGCATCT
GAAACATGTATCTGAACATGTATCTGATGACATGAAGACTCACAGGAACGCTGCCCTGAAGGCTCAGAGTGGTCCAGTAC
GAAGTGGCCCCAAACCGTTCTCTGCTCCTAAACCAGGAGTCAGCCCCTCCCCCAAACCAACCACAAAGAAGGAGCCAGCT
GTACTTGGACTGGAGGGCAAGAAGTGGGGAGTGGAAAGTCAGGAGAATGTTTCCCACCCAATGACTGATGACACGGAGCT
GAAACAGGTGGCTTACATATACAAGTGTGTCAACATGACATTGCAAACCAAGGGCAAAATTAACTCCATTATAGTACATA
ACTGTGAGAAACTCAGTCTGGGGTTTGATGACATGGTGGGCATTATGGAGATAATCAATCGTAGGGATGTCAAAGTTTGG
GTAATGGGTAAAGTGCCAACCATTTTCATCAACAAAACAGATGGCTGCCACATTTACCTGAGCAAGAATTCCCTGGATTG
CAAGATAGTTACTGCCAAA

Alignment

ORF - retro_amel_1891 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.61 %
• Parental protein coverage: 55.13 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSIWTELQAYIKEFHTTGLAWSKTGPMAKELSGLPSGPSAGSGPPPPPPGPPPPPVPTSSGSDDSASRSA
          LS.WTELQAYIK.F..TGLA..KTGP.A...SGLPSGPSAGSGPPPPPP..P..P.P..SGSD.S.S.S.
Retrocopy LSVWTELQAYIKDFCPTGLA*TKTGPVAEQ-SGLPSGPSAGSGPPPPPPDWPSSPSPHHSGSDESTSHSH

Parental  LFAQI-NQGESITHALKHVSDDMKTHRNAALKAQSGPVRSGPKPFSAPKPGVSPSPKPTTKKEPAVLELE
          ........GE...H...HVSDDMKTHRNAALKAQSGPVRSGPKPFSAPKPGVSPSPKPTTKKEPAVL.LE
Retrocopy CSHRL>SGGEHLKHVSEHVSDDMKTHRNAALKAQSGPVRSGPKPFSAPKPGVSPSPKPTTKKEPAVLGLE

Parental  GKKWRVENQENVPNLVIDDTELKQVAYIYKCVNTTLQIKGKINSITVDNCKKLGLVFDDVVGIVEIINSR
          GKKW.VE.QENV.....DDTELKQVAYIYKCVN.TLQ.KGKINSI.V.NC.KL.L.FDD.VGI.EIIN.R
Retrocopy GKKWGVESQENVSHPMTDDTELKQVAYIYKCVNMTLQTKGKINSIIVHNCEKLSLGFDDMVGIMEIINRR

Parental  DVKVQVMGKVPTISINKTDGCHVYLSKNSLDCEIVSAK
          DVKV.VMGKVPTI.INKTDGCH.YLSKNSLDC.IV.AK
Retrocopy DVKVWVMGKVPTIFINKTDGCHIYLSKNSLDCKIVTAK

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_1891 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1891 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004417	1 retrocopy	retro_amel_1891 ,
Bos taurus	ENSBTAG00000013363	1 retrocopy	retro_btau_460,
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Equus caballus	ENSECAG00000024658	1 retrocopy	retro_ecab_119,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Tursiops truncatus	ENSTTRG00000004358	1 retrocopy	retro_ttru_1689,