RetrogeneDB ID: retro_ggal_16

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 3:11666024..11666961(-)
• Located in intron of: ENSGALG00000009158

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSGALG00000003947
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 [Source:RefSeq peptide;Acc:NP_001012610]

Sequence

>retro_ggal_16
ATAGACTGGAGTGGAAAACACAATGGGCCCACCGATACAACCAAGGATGGGACGGTGGTGCAGCTCTGAGGCCTGCCCTT
CGGCTGTAGCAAGGAAGAGATCGTTCAGTTTTTCCAAGGGTTGGAAATCGTGCCAAATAGGATAACATTGACGCTGGACT
ACCAGGGGAGAAGCACAGGTGAGGCCTTCGTGCAGTTTGCTTCAAAGGAGATGGCAGAAAATGCTCCGGGGAAACACAAG
GAAAGAATAGGGCACAGATACACTGAAATCTTTGAAAGTAGTAAGAGTGAAATCAGAGGATTCTCTGACATGCCGAGAAG
AATGATGGGACAACAATGACCTGGACCATATGATAGACCATTACAAGGAAGAGGGGGTTATTATGGAGCTGGGCGTGGAA
GTATGTATGACAGAATGTGTCAAGAAGGTGGTGGATATGATGGTGGATGGATATAGTGGCTTTGTTGACTATGGTGGCTA
CAATAACTATGGCTATGATGACCAAATGAGAGATGGGAGAAGCATGGGAGGACATGGCTATGGAGCTGGAGATGCAGGTT
CAGGTTTCTATGGTGGCAGTCATTTTGTTCACATGAAAAGACTGCCTTTTTGAGCAACAGAAAACAATATTGCAAACTTC
TTCTCACCATTGAATCCTATAAGAGTTCACATTGATATTGGGGCAGATGGAGGAGCCACAGGCAAGGCAGACATGGAATT
TGTAACACATGAGGATGCAGTAGCTGCTACGTACAAGGATAAAAATCACATGCAACATTGATACATTGAACTGTTCCTGA
ATTCAACTGCTGGAGGTGGTTCTGGAATGGGAGGCTACGGCAGAGATGGAACAGATCAAGGTTATGGCTCTGTTGGTAGA
ATGGGTAATAACTACAGTGGTGGTTACAGAATTCCTGATGGCTTGGGCAGCTACAGT

Alignment

ORF - retro_ggal_16 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.94 %
• Parental protein coverage: 92.98 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDWTGKHNGPTDTTNDGTVVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTLDYQGRSTGEAFVQFASKE
          .DW.GKHNGPTDTT.DGTVV.L.GLPFGCSKEEIVQFFQGLEIVPN.ITLTLDYQGRSTGEAFVQFASKE
Retrocopy IDWSGKHNGPTDTTKDGTVVQL*GLPFGCSKEEIVQFFQGLEIVPNRITLTLDYQGRSTGEAFVQFASKE

Parental  IAENALGKHKERIGHRYIEIFKSSKSEIRGFSDMPRRMMGQQRPGPYDRPLGGRGGYYGAGRGSMYDRM-
          .AENA.GKHKERIGHRY.EIF.SSKSEIRGFSDMPRRMMGQQ.PGPYDRPL.GRGGYYGAGRGSMYDRM.
Retrocopy MAENAPGKHKERIGHRYTEIFESSKSEIRGFSDMPRRMMGQQ*PGPYDRPLQGRGGYYGAGRGSMYDRMC

Parental  RRGGGGYDG-GYGGFDDYGGYNNYGYGNDGYDDRMRDGRGMGGHGYGAGDAGSGFHGGGHFVHMRGLPFR
          ..GGG...G.GY.GF.DYGGYNNYGY.....D.R...G.G.G....G.G..G.G.H....FVHM..LPF.
Retrocopy QEGGGYDGG>GYSGFVDYGGYNNYGYDDQMRDGRSMGGHGYGAGDAGSGFYG-GSH----FVHMKRLPF*

Parental  ATENDIANFFSPLNPIRVHIDIGADGRATGEADVEFVTHEDAVAAMSKDKNHMQHRYIELFLNSTAGGGS
          ATEN.IANFFSPLNPIRVHIDIGADG.ATG.AD.EFVTHEDAVAA..KDKNHMQH.YIELFLNSTAGGGS
Retrocopy ATENNIANFFSPLNPIRVHIDIGADGGATGKADMEFVTHEDAVAATYKDKNHMQH*YIELFLNSTAGGGS

Parental  GMGGYGRDGMDQGYGSVGRMGMGNNYSGGYGTPDGLGGYS
          GMGGYGRDG.DQGYGSVGR..MGNNYSGGY..PDGLG.YS
Retrocopy GMGGYGRDGTDQGYGSVGR--MGNNYSGGYRIPDGLGSYS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.57 RPM	103.54 RPM
SRP007412_cerebellum	0.66 RPM	131.96 RPM
SRP007412_heart	0.35 RPM	121.01 RPM
SRP007412_kidney	0.19 RPM	285.58 RPM
SRP007412_liver	0.06 RPM	123.00 RPM
SRP007412_testis	0.12 RPM	344.53 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_16 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_16 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_16 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
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,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647,
Tursiops truncatus	ENSTTRG00000013322	2 retrocopies	retro_ttru_1744, retro_ttru_1766,
Vicugna pacos	ENSVPAG00000011814	1 retrocopy	retro_vpac_403,