RetrogeneDB ID: retro_amel_190

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL192349.1:4526608..4527312(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1orf43
• Ensembl ID: ENSAMEG00000011865
• Aliases: None
• Description: chromosome 1 open reading frame 43 [Source:HGNC Symbol;Acc:29876]

Sequence

>retro_amel_190
GCATCTGGCAGTAACTGGCTGTCCAAGGCCAACGTTGTGGTGGTGAATGTCTACAGGAATCTGGTACACGCAAGCTATTC
AGTTTTAGGAAAAAGCAAATCATGTGTTTTACAAGGAAATCTTGAAGGGGACCTCATGTCCCTTTGGGACCCATGCCCGC
AAAGACTTCAAAGAGGAGACTGATATTCTACTATTCAAACTTTAGGATATCCGGTATGAACCCCAGCTCCTTGGGGATAG
TGATGCAAGGCTGCTACAGCTGGAAACCCAGGGAAATCAGAATTGTTATAATTGTCTGTCTAGGATGAAAGTTCTGGATG
CCATCCATGCTCCTGAGATCCCATTTCAAGCTGAGGATGACATCCCTGTTTCTTTATGGGCATGAACTTCTACCCCTAGC
TACTAGATCTTTGAATCACTAGTACTCCTTTCAAGGGGTTCTCAAAGCTTTCACTATACCCTATCCCTACTGGATGGATG
AGATGGCCCATATGGGACAGGGGTCTGTAGCCAGAGAGAACACTGTTCTATCAGGAGACCCTGACCAAACTGGCCACCAT
GGCCAAGACACAGAGTGGGAGCTCTCAGCAACAACAGTCAGCAGCTGGAGACCTAACGCTATCTCCTAAAATCTCCCCAA
CAACCACCAGGTAACATACCTCCTCTGCAGTTAGAAGAATAAACATGCCAAGCACCTGCTTGAA

Alignment

ORF - retro_amel_190 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.32 %
• Parental protein coverage: 93.68 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ASGSNWLSGVNVVLVMAYGSLVFVL-LFIFVKRQIMRFAMKSRRGPHVPVGH-NAPKDLKEEIDIRLSRV
          ASGSNWLS..NVV.V..Y..LV....LF.F.K.QIM.F..KS.RGPHVP.G...A.KD.KEE.DI.L...
Retrocopy ASGSNWLSKANVVVVNVYRNLVHAS<LFSFRKKQIMCFTRKS*RGPHVPLGP<HARKDFKEETDILLFKL

Parental  QDIKYEPQLLTDGDARLLQLETQGNENCYNYLYRMKALDAIRASEIPFHAE-GRHPRSLMGKNFRSYLLD
          .DI.YEPQLL.D.DARLLQLETQGN.NCYN.L.RMK.LDAI.A.EIPF.AE.G.HP...MG.NF...LLD
Retrocopy *DIRYEPQLLGDSDARLLQLETQGNQNCYNCLSRMKVLDAIHAPEIPFQAE<G*HPCFFMGMNFYP*LLD

Parental  LRNTSTPFKGVRKALIDTLLDGYE-TARYGTGVFGQSEY-LRYQEALSELATVVKARSGSSQRQHQSAAK
          L..TSTPFKG..K........G......YGTGV..Q.E..L.YQE.L..LAT..K..SGSSQ.Q.QSAA.
Retrocopy L*ITSTPFKGFSKLSLYPIPTGWM>DGPYGTGVCSQREH<LFYQETLTKLATMAKTQSGSSQQQ-QSAAG

Parental  DLTQSPEVSPTTI-QVTYLPSSQKSKRAKHFLE
          DLT.SP..SPTT..QVTYL..S.K.K.AKH.LE
Retrocopy DLTLSPKISPTTT<QVTYLLCS*KNKHAKHLLE

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_190 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_190 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 13 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011865	1 retrocopy	retro_amel_190 ,
Callithrix jacchus	ENSCJAG00000009722	1 retrocopy	retro_cjac_175,
Dasypus novemcinctus	ENSDNOG00000019160	1 retrocopy	retro_dnov_2515,
Equus caballus	ENSECAG00000017585	2 retrocopies	retro_ecab_618, retro_ecab_814,
Echinops telfairi	ENSETEG00000001056	15 retrocopies	retro_etel_1138, retro_etel_1318, retro_etel_1388, retro_etel_1633, retro_etel_2182, retro_etel_2205, retro_etel_2206, retro_etel_394, retro_etel_651, retro_etel_719, retro_etel_720, retro_etel_773, retro_etel_842, retro_etel_957, retro_etel_981,
Macropus eugenii	ENSMEUG00000002600	6 retrocopies	retro_meug_1149, retro_meug_1298, retro_meug_1439, retro_meug_1637, retro_meug_213, retro_meug_69,
Myotis lucifugus	ENSMLUG00000013338	1 retrocopy	retro_mluc_537,
Monodelphis domestica	ENSMODG00000017237	3 retrocopies	retro_mdom_1283, retro_mdom_2003, retro_mdom_323,
Otolemur garnettii	ENSOGAG00000012008	2 retrocopies	retro_ogar_2563, retro_ogar_38,
Pteropus vampyrus	ENSPVAG00000002717	1 retrocopy	retro_pvam_696,
Rattus norvegicus	ENSRNOG00000017758	1 retrocopy	retro_rnor_139,
Sarcophilus harrisii	ENSSHAG00000012915	1 retrocopy	retro_shar_740,
Tursiops truncatus	ENSTTRG00000015824	1 retrocopy	retro_ttru_923,