RetrogeneDB ID: retro_itri_748

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393317.1:9805172..9805731(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ITGA10
• Ensembl ID: ENSSTOG00000013934
• Aliases: None
• Description: integrin, alpha 10 [Source:HGNC Symbol;Acc:6135]

Sequence

>retro_itri_748
GCCCACTCCTTTCTTGGCCAAGTGCTGCGGAGACAGGAGGAAAGTCCTGAGTTACAGAAACTGAATGGACAACTGGAGGG
TCATCTGAGCCTTGGAAGAAAGCTTCTGCTGTTGGGTAACTCAGCAGACACCCCTGAGTCAGCCAAGAGAACTGGACACT
CATCAGATGTGGTCTGAGATTCGGCATCACTATTAGCCACCTCAATCGAGCCTTGTACTTCACCTGTGACAATGTCCTGT
GGCCTGAAAAGCCTGGACTAGCTCCCCGCGTGGATCAGGAGAAGTGAACCCAACGTTCATTCAGATCTGTTTTTTTTCCC
TCATCGTGAATCTGAGCCGTGATGTTTATGAGATTTACTTTCTGATCAAACAAGAGTCTTCAGCCTGTAGCTGGTGGTGA
ATGAAGGGTTCCAGAGGAGGAGTTCCAGGAGGAATTGAAACCGGGGGATCTGGGAGACCAGAGATTCCAGGAGGAGGCCT
GCCCCACTCACTGGCTCTGAAGCCTCAGCTCTGAGTCTGCTCCCAGCTTGGGTTCTTCAGAGTCATCTCCTTCTTCTGC

Alignment

ORF - retro_itri_748 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.79 %
• Parental protein coverage: 51.84 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ACSLLGHALQRHGASPELQKQIRLLEGHLSLGRKLLRLGNSADALESAKRAVHLSDVV-LRFCITVSHLN
          A.S.LG..L.R...SPELQK....LEGHLSLGRKLL.LGNSAD..ESAKR..H.SDVV.LRF.IT.SHLN
Retrocopy AHSFLGQVLRRQEESPELQKLNGQLEGHLSLGRKLLLLGNSADTPESAKRTGHSSDVV<LRFGITISHLN

Parental  RALYFACDNVLWAGKSGLAPHVDQEKWAQRSFR-YYLFSLIMNLSRDAYEIRLLMEQESSAGSRR-MKGS
          RALYF.CDNVLW..K.GLAP.VDQEK..QRSFR......LI.NLSRD.YEI..L..QESSA.S...MKGS
Retrocopy RALYFTCDNVLWPEKPGLAPRVDQEK*TQRSFR<IXXXXLIVNLSRDVYEIYFLIKQESSACSWW*MKGS

Parental  GGGGVPGGIEPGGPGGPGTPGGGLP-QLALKLRLRV---LLLARVLRGFC
          ..GGVPGGIE.GG.G.P..PGGGLP..LALK..L.V...L...RV...FC
Retrocopy -RGGVPGGIETGGSGRPEIPGGGLPHSLALKPQL*VCSQLGFFRVISFFC

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_748 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_748 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000013934	1 retrocopy	retro_itri_748 ,