RetrogeneDB ID: retro_amel_783

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192634.1:979921..980407(+)
• Located in intron of: ENSAMEG00000010058

Retrocopy information

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

Parental gene information

• Parental gene symbol: IRAK1BP1
• Ensembl ID: ENSAMEG00000012945
• Aliases: None
• Description: interleukin-1 receptor-associated kinase 1 binding protein 1 [Source:HGNC Symbol;Acc:17368]

Sequence

>retro_amel_783
TGCTGCTGCCTGGACTACATCACGCAGAGCCTCCAGTGGCAGGGTCTGCAGGCAGAAATATAACTGGACAAAGAGTTTTA
GAAGAGCGGAAAATGCTTATCATATGGAAGCAGAGGCCTGCATTACATTTACTGAATTTGGAAAAATACAAAATATTGTA
ACTTGCTTGTTGAACAGCTAGGTAGCTCTGCTGTCATCAGCCAACTCCAGTTCTGTTATACTCCAGGTTCTGTTGAGAAT
CTCAGATAGCGGGCCTGTCTTGTTGTGAACGTGTGGTGCAAAGGCAAGAAGTCTGTAACTTGTTGGCCAAACTCTAGGAA
AACCTTTATTCATCAAAGAAGAAAGAAAAGAATGGGAAGGCTAAATAGATAATCCCCAGTCGTGCAGACTTTCAGGTTCA
TTAACCGCACAATAAAAAACCACAAGTGCAAAATATACGCTGCTTCAAAAGTATTTGTAACTCTTGAAGTAAAGAGGAAA
GAGAAG

Alignment

ORF - retro_amel_783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.68 %
• Parental protein coverage: 64.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  CRRLDYITQSLQQQGLQAE-NVTV-TKDFRRVENAYHMEAEVCITFTEFGKMQNI-CNFLIEKLDSSVVI
          C..LDYITQSLQ.QGLQAE.N.T..TK.FRR.ENAYHMEAE.CITFTEFGK.QNI.CN.L.E.L.SS.VI
Retrocopy CCCLDYITQSLQWQGLQAE<NITG<TKSFRRAENAYHMEAEACITFTEFGKIQNI<CNLLVEQLGSSAVI

Parental  SQPQFYHTPGSVENLRRKACLVAVENAWRKA-QEVCN-LVGQTLGKPLLIKEEETKEWEGQTDDLQSSRL
          SQ.QF..TPGSVENLR..ACLV...N.W.K..QEVCN.LVGQTLGKPL.IKEE..KEWEG..D..QS.RL
Retrocopy SQLQFCYTPGSVENLR*RACLVV--NVWCKG<QEVCN<LVGQTLGKPLFIKEER-KEWEG*IDNPQSCRL

Parental  SSSLTVQQKIKSA-TIHAASKVFITFEVKGKEK
          S.SLT.Q.K..SA..I.AASKVF.T.EVK.KEK
Retrocopy SGSLTAQ*KTTSA<KIYAASKVFVTLEVKRKEK

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_783 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_783 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012945	1 retrocopy	retro_amel_783 ,
Canis familiaris	ENSCAFG00000002793	1 retrocopy	retro_cfam_429,
Monodelphis domestica	ENSMODG00000018444	1 retrocopy	retro_mdom_1885,
Oryctolagus cuniculus	ENSOCUG00000001488	1 retrocopy	retro_ocun_347,