RetrogeneDB ID: retro_amel_1375

Retrocopy location

• Organism: Panda (Ailuropoda melanoleuca)
• Coordinates: GL193282.1:8310..8984(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSAMEG00000018064
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 (2H9) [Source:HGNC Symbol;Acc:5043]

Sequence

>retro_amel_1375
CCAGGACCATAAGACAGACCAATAGGAGGAAAAGGGGCTACTGTAGAGCTAGGCAGGGAAGTATGTACAACAGAATGCCA
CCAGGAGGGGATGGATATGATCACGGTTATGGAGATTTTATGACTATGGTGGCTATAATAATTATGGCTATAGAAATGAT
GGCTTTGATGACAGAATGAGAGACAGGAAGAGGTATGGGAGGACATGGCTATGGCAGAGCTAGTGATAGTGGTCATTTTA
TATATATGAGCGGATCATCTTTTCATGAAGCAGAAAATGACATTGCAAATTTCTTCTCAGCACTAAATCCAATCCAAGTT
CCTACCGATATGGCAGCTGATGGCAGAGCAACAGAAGACATAGAATTTGTGACACATGAAGATGCTGTAGCCGCCGTGTC
TAAAGATAATATGCAACATTGATACATTGAACTTTTCTTGAATTCTCCTGGAGGCAGTTCTGGAATGGAAGGTTCTGGAA
TGGGAGGTTATGGCAGAAAAAGAATGGATAATCAGGGAGGTTATGGATCCGTTGGAAGAATGGGAATAGGTAACAATTAC
AGTGGAGGATATGGTACTCAAGATGGCTTGGGTGGTTATGGCCATGGTGGTGGAGGCAGTGGAGGTTACTATGGGCAAGG
AGGCATGAGTGGAGGTGGATGGCACGGGATGTAT

Alignment

ORF - retro_amel_1375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.99 %
• Parental protein coverage: 68.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PGPYDRPIGGRG-GYYGAGRGSMYDRMRRGGDGYDGGYGGFD-DYGGYNNYGYRNDGFDDRMRD-GRGMG
          PGP.DRPIGG.G.GY..A..GSMY.RM..GGDGYD.GYG.F..DYGGYNNYGYRNDGFDDRMRD.GRGMG
Retrocopy PGP*DRPIGGKG<GYCRARQGSMYNRMPPGGDGYDHGYGDFM<DYGGYNNYGYRNDGFDDRMRD>GRGMG

Parental  GHGYGGAGDASSGFHGGHFVHMRGLPFRATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDA
          GH...G.G.AS.....GHF..M.G..F...ENDIANFFS.LNPI.V..D..ADGRAT...D.EFVTHEDA
Retrocopy GH---GYGRASDS---GHFIYMSGSSFHEAENDIANFFSALNPIQVPTDMAADGRAT--EDIEFVTHEDA

Parental  VAAMSKDKNNMQHRYIELFLNSTPGGSSGMGGSGMGGYGRDGMDNQGGYGSVGRMGMGNNYSGGYGTPDG
          VAA.SKD..NMQH.YIELFLNS.PGGSSGM.GSGMGGYGR..MDNQGGYGSVGRMG.GNNYSGGYGT.DG
Retrocopy VAAVSKD--NMQH*YIELFLNS-PGGSSGMEGSGMGGYGRKRMDNQGGYGSVGRMGIGNNYSGGYGTQDG

Parental  LGGYGRGGGGSGGYYGQGGMSGGGWRGMY
          LGGYG.GGGGSGGYYGQGGMSGGGW.GMY
Retrocopy LGGYGHGGGGSGGYYGQGGMSGGGWHGMY

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_1375 retrocopy.

TSS

Ailuropoda melanoleuca was not studied using FANTOM5 data.

Lab

retro_amel_1375 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Ailuropoda melanoleuca	ENSAMEG00000008888	2 retrocopies	retro_amel_57, retro_amel_9,
Ailuropoda melanoleuca	ENSAMEG00000018064	1 retrocopy	retro_amel_1375 ,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Equus caballus	ENSECAG00000007190	1 retrocopy	retro_ecab_912,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Mustela putorius furo	ENSMPUG00000011997	1 retrocopy	retro_mputfur_1469,
Oryctolagus cuniculus	ENSOCUG00000004443	3 retrocopies	retro_ocun_1136, retro_ocun_1379, retro_ocun_1615,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,