RetrogeneDB ID: retro_amel_1913

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL195778.1:6829..7220(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CWC15
• Ensembl ID: ENSAMEG00000011392
• Aliases: None
• Description: CWC15 spliceosome-associated protein homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:26939]

Sequence

>retro_amel_1913
AATATAGATTCTCTAACATAAGAACATACAATCTTCTCTTCAGTGTCAAAGAAGTCTTGCTTAGACCAGATTCCTGCTGT
CAACCTTGATGCAGATGATCTTCCAACAGATTGGGAAGATGAAAATGAAAATTTTGAAGAGGGGAGTGATGATAATCACC
TTTTGCAGAATTAGAAAAAAATAAAAATGAAGGAGCTGAGATCAGTCCAGGAATGAACAAGAAGAGAAAACTGAAGAAGA
AAGAATACATATGGAAAACATTTTGAGTGGAAACCCTCTCAATCTCACTGGCCCATCACAATTTCAGGCCAACTTCAAAG
TTAAAAGAAAGTAGGATGATGATGCTGTTTTCAAGAACTGTGCAAATGGTGTAGATTATCAGAAGAAAGAC

Alignment

ORF - retro_amel_1913 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.69 %
• Parental protein coverage: 58.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NRDRPAREHTTSSSVSKKPRLDQIPAANLDADDPLTDEEDEDEDFEEESDDDDTAALL-AELEKIKKERA
          N.D....EHT..SSVSKK..LDQIPA.NLDADD..TD.EDE....E......D...LL.AEL.....E.A
Retrocopy NIDSLT*EHTIFSSVSKKSCLDQIPAVNLDADDLPTDWEDEN---ENFEEGSDDNHLL<AELXXXXXEGA

Parental  E-EQARKEQEQKAEEERIRMENILSGNPLLNLTGPSQPQANFKVKRRWDDDVVFKNCAKGVDDQKKD
          E..Q.R.EQE.K.EEERI.MENILSGNP.LNLTGPSQ.QANFKVKR..DDD.VFKNCA.GVD.QKKD
Retrocopy E<DQSRNEQEEKTEEERIHMENILSGNP-LNLTGPSQFQANFKVKRK*DDDAVFKNCANGVDYQKKD

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_1913 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1913 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 12 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011392	1 retrocopy	retro_amel_1913 ,
Bos taurus	ENSBTAG00000007913	1 retrocopy	retro_btau_703,
Canis familiaris	ENSCAFG00000004134	6 retrocopies	retro_cfam_1329, retro_cfam_2123, retro_cfam_503, retro_cfam_537, retro_cfam_61, retro_cfam_805,
Dipodomys ordii	ENSDORG00000011075	1 retrocopy	retro_dord_313,
Echinops telfairi	ENSETEG00000006649	1 retrocopy	retro_etel_647,
Felis catus	ENSFCAG00000007826	1 retrocopy	retro_fcat_1416,
Myotis lucifugus	ENSMLUG00000002032	3 retrocopies	retro_mluc_102, retro_mluc_2143, retro_mluc_2478,
Ornithorhynchus anatinus	ENSOANG00000010404	1 retrocopy	retro_oana_5,
Oryctolagus cuniculus	ENSOCUG00000001629	4 retrocopies	retro_ocun_1037, retro_ocun_1605, retro_ocun_679, retro_ocun_743,
Rattus norvegicus	ENSRNOG00000008490	3 retrocopies	retro_rnor_2452, retro_rnor_251, retro_rnor_476,
Sarcophilus harrisii	ENSSHAG00000016534	5 retrocopies	retro_shar_26, retro_shar_333, retro_shar_447, retro_shar_596, retro_shar_768,
Tarsius syrichta	ENSTSYG00000000407	1 retrocopy	retro_tsyr_1585,