RetrogeneDB ID: retro_amel_429

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192440.1:1675522..1675981(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSAMEG00000016936
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LGALSL
• Ensembl ID: ENSAMEG00000001067
• Aliases: None
• Description: lectin, galactoside-binding-like [Source:HGNC Symbol;Acc:25012]

Sequence

>retro_amel_429
GATGATGGGTGTTTAAACAACTCCTTGGGCTCTCCAGTAGGAGATTGTGGTACTTCCCACGACTGAGAGTTCCATGTGTG
GGCACATGAAAGCTGCCACAAGACCAGGCAAGAAGGTGTTGGTGGTGGGCACTGCAGACCACAAGCCAGAGAGCTTTGCC
ATCAGATTGCCCTCTGGTGACTCTGAAGACCCTGCCACCAATGTGGCAACTGAACGCAAAGCTGTGTTCACAGGCCGGCA
GCTACTCAAAGTTGCTTGTGTATCTGAAGAACGGTCGGCCATCCCTCACTTTCCATTCATCCCAGACCAGCCACGCAGGG
TGGAAATTCTCTGTGAGCACTTATGTTTCAGAGTGTCTGTGGATGGACACCAACTTTTTTATTTTTACCACCGCATTCAA
ATGTTATCTGCAGTTGCTACCATAAAGATAAACGGGGATTCCAGATCGCTCTGCTTGGC

Alignment

ORF - retro_amel_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.7 %
• Parental protein coverage: 91.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDGHLNNS-LGSPVQADVYFPRLIVP-FCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPAD
          DDG.LNNS.LG.......YFPRL.VP..CGH.K...RPGKKVLV.G..D..PESFAI.L..GDSEDP...
Retrocopy DDGCLNNS<LGLSSRRLWYFPRLRVP<MCGHMKAATRPGKKVLVVGTADHKPESFAIRLPSGDSEDPATN

Parental  VAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQLFDFYHRIQ
          VA.E.KAVFT.RQLL...C.S....EE.SAIP.FPFIPDQP.RVEILCEH..FRV.VDGHQLF.FYHRIQ
Retrocopy VATERKAVFTGRQLLKVACVS----EERSAIPHFPFIPDQPRRVEILCEHLCFRVSVDGHQLFYFYHRIQ

Parental  TLSAIDTIKINGD-LQITKLG
          .LSA..TIKINGD..QI..LG
Retrocopy MLSAVATIKINGD<FQIALLG

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_429 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_429 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001067	1 retrocopy	retro_amel_429 ,
Ailuropoda melanoleuca	ENSAMEG00000009910	1 retrocopy	retro_amel_785,
Bos taurus	ENSBTAG00000000156	1 retrocopy	retro_btau_1263,
Dasypus novemcinctus	ENSDNOG00000015222	1 retrocopy	retro_dnov_493,
Felis catus	ENSFCAG00000001209	1 retrocopy	retro_fcat_1280,
Monodelphis domestica	ENSMODG00000003226	2 retrocopies	retro_mdom_1350, retro_mdom_233,
Mus musculus	ENSMUSG00000042363	3 retrocopies	retro_mmus_1637, retro_mmus_272, retro_mmus_2942,
Sarcophilus harrisii	ENSSHAG00000011885	2 retrocopies	retro_shar_315, retro_shar_732,