RetrogeneDB ID: retro_itri_1537

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393533.1:1172540..1173745(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSBPL9
• Ensembl ID: ENSSTOG00000000692
• Aliases: None
• Description: oxysterol binding protein-like 9 [Source:HGNC Symbol;Acc:16386]

Sequence

>retro_itri_1537
AGTCGACATTCACCACATAGTAGCAGTCTAACTTCTCCATGTCACGTCACCTTGTCTCCAAATACAATCCCAGAGTTTTC
TAACTGTAGCAGTGAAGATGAATTCTATGATGCTGATGAATTCTATCAGAGTGGCTCATCCCCAAAACGGTTAATATATT
CTTCTGGTTCTGCCTCAGTCTTGACACATAGCAGTTCGTGAAATAGCCTAAAGCACCCAGAAACCACAGAATCACTGAAT
TCTTGCATGTCCAATGGTACAAGTGATGCTGACCTTTTTGATTCACATGACTGATAGAGACCATGATGGGGAGGCAGGAT
CAGTGGAAGAGCACAAGAGTGTTATCATGCACTTCTTGTCACAAGTTAGGCTCGGAATGGATCTTACTAAGGTAGTTCTT
CCAACATTTATTCTTGAAAGAAGATCTCTTTTAGGAATGTATGCAGACTTTTTTTGCACATCCAGACCTGTTTGTGAGCA
TTAGTGACCAGAAAGATCCCAGGGATCGAATGGTTCAGGATGTGAAATGGTACCTCTCTGCCTTTCATGCAGGAAGGAAA
GGATCAGTTGCCAAAAAGCTATACAACCCCATTTTGGGTGAGATCTTTCAGTATCACTGGACATTACCAAATGACACTGA
AGAGAACACAGAGCTAGTTTCAGAAGGACTGGTTCCCTAGGTTTCCAAAAACAGTGTAACAAAAGTGGCTGAGCAGGTTT
CCTATCATCCACCCATTTCAGCCTTTTATGCTGACTGTTTTAATAAGAAAATCCAATTCAATGCTCATATCTGGACTAAA
TCAAAATTCCTTGGGATTTCAATTGGGGTGCATAACATAGGGCAAGGCTGTGTCTCATGTCTAGACTATGATGAGCATTA
CATTCTCATATTCCCCAATGGTTATGGAAGGTCTATCCTCACAGTGCCCTGGGTGGAACTAGGAGGAGAATGCAATATTA
ATTGTTCCAAAACTGGTTATAGTGCAAATATCATCTTCCACACTAAACCTTTCTATGGAGGCAAGAAATACAGAATTACT
GCTGAGTTTTTTTCTCCAAATGACAAGAAGTCTTTTTGCTCAATTGAAGGGGAATGGAATGGTGTAATGTATGCAAAATA
TGAAACAGGGGAAAATACAGTCTTTGTAGATACCAAGAAGTTGCCTATAATCAAGAAAAAAGTGAGGAAGTTGGAAGATC
AGAAT

Alignment

ORF - retro_itri_1537 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.81 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SGHSPPSSSLTSPSHVNLSPNTVPEFSYSSSEDEFYDADEFHQSGSSPKRLIDSSGSASVLTHSSSGNSL
          S.HSP.SSSLTSP.HV.LSPNT.PEFS..SSEDEFYDADEF.QSGSSPKRLI.SSGSASVLTHSSS.NSL
Retrocopy SRHSPHSSSLTSPCHVTLSPNTIPEFSNCSSEDEFYDADEFYQSGSSPKRLIYSSGSASVLTHSSS*NSL

Parental  KRPDTTESLNSSMSNGTSDADLFDSHD-DRDDDGEAGSVEEHKSVIMHLLSQVRLGMDLTKVVLPTFILE
          K.P.TTESLNS.MSNGTSDADLFDSHD.DRD.DGEAGSVEEHKSVIMH.LSQVRLGMDLTKVVLPTFILE
Retrocopy KHPETTESLNSCMSNGTSDADLFDSHD>DRDHDGEAGSVEEHKSVIMHFLSQVRLGMDLTKVVLPTFILE

Parental  RRSLLEMYAD-FFAHPDLFVSISDQKDPRDRMVQVVKWYLSAFHAGRKGSVAKKPYNPILGEIFQCHWTL
          RRSLL.MYAD.FFAHPDLFVSISDQKDPRDRMVQ.VKWYLSAFHAGRKGSVAKK.YNPILGEIFQ.HWTL
Retrocopy RRSLLGMYAD>FFAHPDLFVSISDQKDPRDRMVQDVKWYLSAFHAGRKGSVAKKLYNPILGEIFQYHWTL

Parental  PNDTEENTELVSEGPVPWVSKNSVTFVAEQVSHHPPISAFYAECFNKKIQFNAHIWTKSKFLGMSIGVHN
          PNDTEENTELVSEG.VP.VSKNSVT.VAEQVS.HPPISAFYA.CFNKKIQFNAHIWTKSKFLG.SIGVHN
Retrocopy PNDTEENTELVSEGLVP*VSKNSVTKVAEQVSYHPPISAFYADCFNKKIQFNAHIWTKSKFLGISIGVHN

Parental  IGQGCVSCLDYDEHYILTFPNGYG-SILTVPWVELGGECNINCSKTGYSANIVFHTKPFYGGKKHRITAE
          IGQGCVSCLDYDEHYIL.FPNGYG.SILTVPWVELGGECNINCSKTGYSANI.FHTKPFYGGKK.RITAE
Retrocopy IGQGCVSCLDYDEHYILIFPNGYGRSILTVPWVELGGECNINCSKTGYSANIIFHTKPFYGGKKYRITAE

Parental  IFSPNDKKSFCSIEGEWNGVMYAKYATGENTVFVDTKKLPIIKKKVRKLEDQN
          .FSPNDKKSFCSIEGEWNGVMYAKY.TGENTVFVDTKKLPIIKKKVRKLEDQN
Retrocopy FFSPNDKKSFCSIEGEWNGVMYAKYETGENTVFVDTKKLPIIKKKVRKLEDQN

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_1537 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1537 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021574	1 retrocopy	retro_cjac_1235,
Felis catus	ENSFCAG00000010298	1 retrocopy	retro_fcat_1134,
Gorilla gorilla	ENSGGOG00000004787	1 retrocopy	retro_ggor_737,
Microcebus murinus	ENSMICG00000002731	1 retrocopy	retro_mmur_1035,
Myotis lucifugus	ENSMLUG00000009199	1 retrocopy	retro_mluc_2149,
Nomascus leucogenys	ENSNLEG00000016138	2 retrocopies	retro_nleu_1820, retro_nleu_279,
Oryctolagus cuniculus	ENSOCUG00000004303	1 retrocopy	retro_ocun_281,
Pongo abelii	ENSPPYG00000001358	2 retrocopies	retro_pabe_689, retro_pabe_787,
Pan troglodytes	ENSPTRG00000000730	1 retrocopy	retro_ptro_632,
Ictidomys tridecemlineatus	ENSSTOG00000000692	1 retrocopy	retro_itri_1537 ,