RetrogeneDB ID: retro_amel_1661

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193891.1:168929..169207(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: INIP
• Ensembl ID: ENSAMEG00000006841
• Aliases: None
• Description: INTS3 and NABP interacting protein [Source:HGNC Symbol;Acc:24994]

Sequence

>retro_amel_1661
AATTACCAACAGGTCTTGGCAGGACTGGGCAGAGAGAAAAGACAATTGCTGATGCAGGGCCCGTCTTCAACAAACCATCC
TGGAGCTGGAGTGGGCACTGCATCCCCGAGACCCTCTCTTGACAAGGACTTCGGGATGGCGATCAGCAGTCGCCTACCGC
TGCCCCGCAAAGGGCGGCTTTGTAGCACGCACACCCACATTTGTCTGGGTACCTCTTGACTCGAGAGTGTGGTTGGGGGA
AACTTCTTCTTCCCGTTCTCCCTCACCTTGACCCAGAA

Alignment

ORF - retro_amel_1661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.51 %
• Parental protein coverage: 94.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NRVAILAELDKEKRKLLMQNQSSTNHPGASI--ALSRPSLNKDF-RDHAEQQHIAAQQKAALQHAHAHSS
          N....LA.L..EKR.LLMQ..SSTNHPGA....A..RPSL.KDF.RD...Q...AA.Q.AAL.HAH.H.S
Retrocopy NYQQVLAGLGREKRQLLMQGPSSTNHPGAGVGTASPRPSLDKDF<RDGDQQSPTAAPQRAAL*HAHPHLS

Parental  GYFITQDSAFGNLILPVLPRLDPE
          GY..T.....G.L.LPVLP.LDPE
Retrocopy GYLLTRECGWGKLLLPVLPHLDPE

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_1661 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1661 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006841	1 retrocopy	retro_amel_1661 ,
Equus caballus	ENSECAG00000008524	1 retrocopy	retro_ecab_187,
Homo sapiens	ENSG00000148153	1 retrocopy	retro_hsap_2980,
Microcebus murinus	ENSMICG00000001130	1 retrocopy	retro_mmur_92,
Nomascus leucogenys	ENSNLEG00000016554	1 retrocopy	retro_nleu_1508,
Oryctolagus cuniculus	ENSOCUG00000016717	1 retrocopy	retro_ocun_335,
Oryzias latipes	ENSORLG00000011577	1 retrocopy	retro_olat_8,
Pan troglodytes	ENSPTRG00000023472	1 retrocopy	retro_ptro_2015,
Sorex araneus	ENSSARG00000003661	1 retrocopy	retro_sara_104,
Xiphophorus maculatus	ENSXMAG00000002259	1 retrocopy	retro_xmac_8,