RetrogeneDB ID: retro_amel_566

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192505.1:1550743..1551344(+)
• Located in intron of: ENSAMEG00000015612

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSAMEG00000010115
• Aliases: None
• Description: None

Sequence

>retro_amel_566
GAACAGAGGCTGAAGCGGAATGAAGATCGAAAGTTAAATCACCAGGAAGCTGTGGAGGAAGATAAAAGACTTAAATTACC
AAAAACTGGGAGGCTAAAAAAGCTCGTTTGGAATGGGAGCTGCAGGAAGAAGAAAAGAAAAAAGAATGTGCAGCAAGAGG
GGTGGACTATGAGTAAGTGAAGCTACTGGAGACAGGGCAGAAGAGGCAGAAAGATGGGAGAGGAAGAAGAGGAGGAAAAA
CCCTGACCTGGGATTCTCAGATTGTGCTGCTGCCCCCTTACGCCAGTATTATTGGCTGACCAAGCGGACCAAACCTGACA
TGGAAACTTATGAGAGACTGAGAGAAAAACACGGAGAGGCGTTCTACCCAACGTCCGACAGTCTTCTTCATGGAACACAT
GTGCCCTCCACAGAGTAGACTAATAGGATGGTCATAGACTTGGAAAAGCAAACTGAAAAACGAGACCCGTATAGCCGTCC
TTATAATGATGATGCAGACATTGACTACATTAATTAAAGAAAAGCCAAATTCAACATGAAGGCAGAAAGATTCTATGGGA
AATATACAGCTAAACAGAACTTAGAAAGAGGAACAGCAGTC

Alignment

ORF - retro_amel_566 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.09 %
• Parental protein coverage: 84.36 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ELHLKRNEARKLNHQEVVEEDKRLKLPA-NWEARKARLEWELQEEEKKKECAARGEDYEKVKLLEIS-AE
          E..LKRNE.RKLNHQE.VEEDKRLKLP..NWEA.KARLEWELQEEEKKKECAARG.DYE.VKLLE...AE
Retrocopy EQRLKRNEDRKLNHQEAVEEDKRLKLPK<NWEAKKARLEWELQEEEKKKECAARGVDYE*VKLLETG<AE

Parental  DAERWERKKRRKNPDLGFSDYAAAQLRQYHRLTKQIKPDMETYERLREKHGEEFFPTSNSLLHGTHVPST
          .AERWERKKRRKNPDLGFSD.AAA.LRQY..LTK..KPDMETYERLREKHGE.F.PTS.SLLHGTHVPST
Retrocopy EAERWERKKRRKNPDLGFSDCAAAPLRQYYWLTKRTKPDMETYERLREKHGEAFYPTSDSLLHGTHVPST

Parental  EEVDRMVMDLEKQIEKRDKYSRRRPYNDDADIDYINERNAKFNKKAERFYGKYTAEIKQNLERGTAV
          E...RMV.DLEKQ.EKRD.YS..RPYNDDADIDYIN.R.AKFN.KAERFYGKYTA..KQNLERGTAV
Retrocopy E*TNRMVIDLEKQTEKRDPYS--RPYNDDADIDYIN*RKAKFNMKAERFYGKYTA--KQNLERGTAV

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_566 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_566 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010115	1 retrocopy	retro_amel_566 ,
Bos taurus	ENSBTAG00000001651	1 retrocopy	retro_btau_478,
Choloepus hoffmanni	ENSCHOG00000005273	1 retrocopy	retro_chof_2034,
Callithrix jacchus	ENSCJAG00000018559	1 retrocopy	retro_cjac_467,
Homo sapiens	ENSG00000117614	1 retrocopy	retro_hsap_4152,
Monodelphis domestica	ENSMODG00000013951	1 retrocopy	retro_mdom_899,
Oryctolagus cuniculus	ENSOCUG00000013050	1 retrocopy	retro_ocun_1522,
Sarcophilus harrisii	ENSSHAG00000007152	1 retrocopy	retro_shar_15,