RetrogeneDB ID: retro_itri_647

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:14466313..14466858(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPH3
• Ensembl ID: ENSSTOG00000011676
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein H3 (2H9) [Source:HGNC Symbol;Acc:5043]

Sequence

>retro_itri_647
TCTGAAGTAAAAGGAACATTTAAATCAAATGGTATTGAGATGGATTGAGTTATGAAATAGAATGGTCCAAATGACACTAG
TGATAGGACAGTATGACTATGGGGACTGCCATTTGGTTGCAGCAAAGAGGAAAGTGTTCAGTTCTTTCAAGGGTTGGAAA
TTGTGCCAAATGGGATAATGGTGATGATGGACTACCAAGAGAGAAGCACAGAGGAGGCCTTTGTGCCATTTGCTTCAAAG
GAGATAGCAGAAAATGCTCTGGGGGGAAACACAGGAAAGAATAGGGCACAAGTATATTGAGATCTTCAGAAGTAGCAAGA
GTGAAATCAAAGAATTTTATGACCCACCAAGAAGATTGCTGGGACAGCTACCAGAACTACATGATAGACCAATAGGAGAA
AGAGGTGGTTATTATGGAGCTGGGTGTGGAAGTACCTATGATAGAATGTGACAAGGAGGTGATGGAAATGATGTAGTTAT
GGAGGTTTTGATGACTATTGTGGCTATAATAATTAGGCTATGGAAAGGATGGCTTGGATGACAGG

Alignment

ORF - retro_itri_647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.22 %
• Parental protein coverage: 52.3 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NRIMQAFKSNGIEMDWVMKHNGPNDASDGTVRLRGLPFGCSKEEIVQFFQGLEIVPNGITLTMDYQGRST
          ......FKSNGIEMD.VMK.NGPND.SD.TV.L.GLPFGCSKEE.VQFFQGLEIVPNGI...MDYQ.RST
Retrocopy SEVKGTFKSNGIEMD*VMK*NGPNDTSDRTV*LWGLPFGCSKEESVQFFQGLEIVPNGIMVMMDYQERST

Parental  GEAFVQFASKEIAENAL-GKHKERIGHRYIEIFRSSRSEIKGFYDPPRRLLGQRPGPYDRPIGGRGGYYG
          .EAFV.FASKEIAENAL.G...ERIGH.YIEIFRSS.SEIK.FYDPPRRLLGQ.P...DRPIG.RGGYYG
Retrocopy EEAFVPFASKEIAENAL>GETQERIGHKYIEIFRSSKSEIKEFYDPPRRLLGQLPELHDRPIGERGGYYG

Parental  AGRGSMYDRMRRGGDGYD-GGYGGFDDYGGYNN-YGYGNDGFDDR
          AG.GS.YDRM..GGDG.D...YGGFDDY.GYNN..GYG.DG.DDR
Retrocopy AGCGSTYDRM*QGGDGND<CSYGGFDDYCGYNN<LGYGKDGLDDR

Legend:

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

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_647 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_647 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000010365	1 retrocopy	retro_acar_184,
Bos taurus	ENSBTAG00000014316	2 retrocopies	retro_btau_1504, retro_btau_470,
Callithrix jacchus	ENSCJAG00000019154	2 retrocopies	retro_cjac_292, retro_cjac_578,
Gallus gallus	ENSGALG00000003947	1 retrocopy	retro_ggal_16,
Macropus eugenii	ENSMEUG00000013139	1 retrocopy	retro_meug_1627,
Ictidomys tridecemlineatus	ENSSTOG00000011569	2 retrocopies	retro_itri_1828, retro_itri_523,
Ictidomys tridecemlineatus	ENSSTOG00000011676	1 retrocopy	retro_itri_647 ,
Ictidomys tridecemlineatus	ENSSTOG00000016376	2 retrocopies	retro_itri_66, retro_itri_78,