RetrogeneDB ID: retro_itri_501

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393296.1:6903064..6903728(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LDHB
• Ensembl ID: ENSSTOG00000022058
• Aliases: None
• Description: lactate dehydrogenase B [Source:HGNC Symbol;Acc:6541]

Sequence

>retro_itri_501
GTTGTGACCCTTAAGGAAAAGCTCACTGCACCAGTTGCAGAAGAGAAGGCAGAAGTTCCCAAACAATAAGATCACTGTAA
TGGCTGTTGGACAAGTCGATATGGCGTGTGCAATCAGCATTCTGGGAATTTCTCTGGCTGATGAACTTGCCCTGGTGGAT
GATTTAGAAGATAAGCTCAAAGGAGACAGGATGGATCTGCAGCATGAAGCTTATTTCTTCAAACACCCAAAACTGTAGCA
GATAAAGTTTAGTCAGTGACTGCCAGTTCTAAGATCGTGATAGTAACTGCAGGAGTCCGTCGGCAGGAGCGGGGCAGTTG
TCTCAATCTGGTGCAGAGAAATGTCAATGTCTTCAGATTCATTATTCCTCAGATCATCAAGCACAGTCTCTCAATGGCAT
CATAATTGTGATTTCCAACCCAGTGGACATTCTTACATATGTTACCTGGAAACTAAGTGGATTACCCAACACCGTGTGAT
TAGAAGGGAGTGCAGTCTGGCTTCTGCTAGATTTTGCTATTTTATGGCTGAGAAACTTGGCATTCATCCTAGCAGCTGCC
ATGAATGGATTCTGGGAGAACATGGCGACTCAAGTGTGGCTGTGTGGAGTGGAGTCAACGTGGCTGGTAGTTCTCTCCAG
GAACTAAATCCAGAAATGGGAACA

Alignment

ORF - retro_itri_501 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.96 %
• Parental protein coverage: 66.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MATLKEKLIAPVAEEETTVP-NNKITVVGVGQVGMACAISILGKSLADELALVDVLEDKLKGEMMDLQHG
          ..TLKEKL.APVAEE...VP.NNKITV..VGQV.MACAISILG.SLADELALVD.LEDKLKG..MDLQH.
Retrocopy VVTLKEKLTAPVAEEKAEVP>NNKITVMAVGQVDMACAISILGISLADELALVDDLEDKLKGDRMDLQHE

Parental  -SLFLQTPKIVADKVTSVTVNNEMVVVTAGVRQQEGESRLNLVQRNVNVFKFIIPQIVKYSPDCI-IIVV
          .SLFLQTPK.VADKV.SVT.....V.VTAGVR.QE..S.LNLVQRNVNVF.FIIPQI.K.S.....II.V
Retrocopy <SLFLQTPKTVADKV*SVTASSKIVIVTAGVRRQERGSCLNLVQRNVNVFRFIIPQIIKHSLSMA<IIIV

Parental  -SNPEYSVDILTYVTWKLSGLP-KHRVIGSGCNLDSARFRYLMAEKLGIHPSSCHGWILGEHGDSSVVAV
          .SNP...VDILTYVTWKLSGLP..HRVI...C.L.SARF.Y.MAEKLGIHPSSCH.WILGEHGDSS.VAV
Retrocopy ISNP---VDILTYVTWKLSGLP<QHRVIRRECSLASARFCYFMAEKLGIHPSSCHEWILGEHGDSS-VAV

Parental  WSGVNVAGVSLQELNPEMGT
          WSGVNVAG.SLQELNPEMGT
Retrocopy WSGVNVAGSSLQELNPEMGT

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_501 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_501 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 16 parental genes, and 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016175	4 retrocopies	retro_amel_1316, retro_amel_814, retro_amel_882, retro_amel_977,
Bos taurus	ENSBTAG00000019603	4 retrocopies	retro_btau_1589, retro_btau_303, retro_btau_451, retro_btau_647,
Canis familiaris	ENSCAFG00000012195	9 retrocopies	retro_cfam_1068, retro_cfam_111, retro_cfam_1674, retro_cfam_17, retro_cfam_1700, retro_cfam_174, retro_cfam_1836, retro_cfam_701, retro_cfam_93,
Cavia porcellus	ENSCPOG00000007138	1 retrocopy	retro_cpor_762,
Echinops telfairi	ENSETEG00000019955	1 retrocopy	retro_etel_850,
Felis catus	ENSFCAG00000012639	1 retrocopy	retro_fcat_462,
Macropus eugenii	ENSMEUG00000004825	1 retrocopy	retro_meug_311,
Myotis lucifugus	ENSMLUG00000012155	1 retrocopy	retro_mluc_202,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Monodelphis domestica	ENSMODG00000017786	1 retrocopy	retro_mdom_1484,
Mustela putorius furo	ENSMPUG00000000172	5 retrocopies	retro_mputfur_1300, retro_mputfur_1561, retro_mputfur_492, retro_mputfur_539, retro_mputfur_549,
Oryctolagus cuniculus	ENSOCUG00000022015	1 retrocopy	retro_ocun_805,
Sorex araneus	ENSSARG00000002565	1 retrocopy	retro_sara_713,
Sus scrofa	ENSSSCG00000000576	1 retrocopy	retro_sscr_37,
Ictidomys tridecemlineatus	ENSSTOG00000000014	3 retrocopies	retro_itri_1396, retro_itri_1526, retro_itri_535,
Ictidomys tridecemlineatus	ENSSTOG00000022058	2 retrocopies	retro_itri_501 , retro_itri_648,