RetrogeneDB ID: retro_itri_429

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393291.1:3482172..3483311(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM149B1
• Ensembl ID: ENSSTOG00000002142
• Aliases: None
• Description: family with sequence similarity 149, member B1 [Source:HGNC Symbol;Acc:29162]

Sequence

>retro_itri_429
GCAATATCCCCTGGTTTGTGTGCTGTGGAAAGAGAAGAAGACTGTATAATCTTCTCAGAAGGAATAGTTGAGGAATACCT
AGCTTTCGACAATACAGATATGGAAGAGAGATTTCATGAAAATAAATCAGAAGCAGCTACAAAGAAACAGAAATTAGGGT
ACCCTCCCATTGCTCCATTTTACTCCATGAAAGAGGAAATTCTTGCTTATGTGTTTCGCAAAGTGTGGAGCAAAACTGTG
AGCTGTTTGGAGCAATTGACACGTAGTTACCGGGAAGGATTTGCTTCTGATGATGAGAGTAATGTTGCAGTCACCAGACC
AGATTCAGAAAGTCTCTATGTGCTGAGTGAACCACATACTTTGGTGTTACCTCCAGTGCCACAGTCCAAGGTGCTATCTG
TCACCTCGGATCTGATGAGTCTCTGTCAAGCAAGTGGTCATCAGCCAAATGCGAATGGTCTCTTGATTCATGGGATGCCT
CTAAAGCCAAGAAATCTCTACCCAATTGACAAGCTCCTAGATCTTGATGACAAGCTACTTATGAGGCCTGGGTCCAGTAC
CATTTTTTCAACCTGAAATTGGCCAAACCAAGCCTTGGAGCTTAGTACATCATGTCTGTCATATATAAAGTGCAGTCTGC
CAGGAGACGTAATCCCCCACCACGTACCCTTCATCCAATCAGCACAAGCCACTCACGCACTGGAACACCAAGACCTGTGG
AAGAAATCCTCAGAGGATCACAAGTCCCTTTGGCAGTTGACTGGCTCTCCTCTCGCTCACCAATACCCCTGAGTCGAAAT
AATCTGCTGCCACCTATTGGCACAAGCGAAGTGGAACACCTGAGCCCTGTGGAGCCACAAAGGCAAATGAAACCCCATGG
TGATTCCAGTCGAGCCCGAAGTGCAGTGGTGGATGAGCCTAACCATCAACAGCCTCAAGATAGGCTCCTTTTATCTAACT
TCTTCTCCAGGCCCAATACAACTCGGTCATTTATGCCAGAAACACAGTATCATCGTTCACATGCACTTGAATACCCTCAT
CAAGCCCGACCCAGTAGGTGATCTGCAGGTCCTCATTTGCATGCCTCTACAAAAATCTCAAAGCAGAGGTGGCCAATCTC
TAAAACCAGGCAGGGACCA

Alignment

ORF - retro_itri_429 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.32 %
• Parental protein coverage: 65.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ARSPGLCAVEREEDCTIFSEGIIEEYLAFDHTDMEEGFHENKSEAATKKQKLGYPPIAPFYCIKEDILAY
          A.SPGLCAVEREEDC.IFSEGI.EEYLAFD.TDMEE.FHENKSEAATKKQKLGYPPIAPFY..KE.ILAY
Retrocopy AISPGLCAVEREEDCIIFSEGIVEEYLAFDNTDMEERFHENKSEAATKKQKLGYPPIAPFYSMKEEILAY

Parental  VFDNVWSKIVSCLAQLTRSHWEGFASDDESNVAVTRPDSESPYVLSEPHTLVLPPVPQSKVLSVTSNLMS
          VF..VWSK.VSCL.QLTRS..EGFASDDESNVAVTRPDSES.YVLSEPHTLVLPPVPQSKVLSVTS.LMS
Retrocopy VFRKVWSKTVSCLEQLTRSYREGFASDDESNVAVTRPDSESLYVLSEPHTLVLPPVPQSKVLSVTSDLMS

Parental  LCQASGHQPNANGLLIHGMPLQPRNLYLIDKLLDLDDKLLMRPGSSTIFSTRNWPNRALELSTSCLSYKV
          LCQASGHQPNANGLLIHGMPL.PRNLY.IDKLLDLDDKLLMRPGSSTIFST.NWPN.ALELSTSCLSY..
Retrocopy LCQASGHQPNANGLLIHGMPLKPRNLYPIDKLLDLDDKLLMRPGSSTIFST*NWPNQALELSTSCLSYIK

Parental  QS-ARRRNPP-PRTLHPISTSHSCTGTPRPVEEILRGSQVPLAVVDSLSSPSPIPLSRNNLLPPIGTSEV
          .S...RR..P.PRTLHPISTSHS.TGTPRPVEEILRGSQVPLA.VD.LSS.SPIPLSRNNLLPPIGTSEV
Retrocopy CS<SARRRNPPPRTLHPISTSHSRTGTPRPVEEILRGSQVPLA-VDWLSSRSPIPLSRNNLLPPIGTSEV

Parental  EHLSPVGPQRQMKPHGDSSRARSAVVDEPNYQQPQDRLLLSNFFSRPNTTQSFMPETQYHRSHALEYPHQ
          EHLSPV.PQRQMKPHGDSSRARSAVVDEPN.QQPQDRLLLSNFFSRPNTT.SFMPETQYHRSHALEYPHQ
Retrocopy EHLSPVEPQRQMKPHGDSSRARSAVVDEPNHQQPQDRLLLSNFFSRPNTTRSFMPETQYHRSHALEYPHQ

Parental  TRPSRGSAGSHLHAS-QKSQSRGG-PISKTRQGP
          .RPSR.SAG.HLHAS.QKSQSRGG.PISKTRQGP
Retrocopy ARPSR*SAGPHLHAS>QKSQSRGG<PISKTRQGP

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_429 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_429 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000138286	1 retrocopy	retro_hsap_1529,
Macaca mulatta	ENSMMUG00000011281	1 retrocopy	retro_mmul_2158,
Nomascus leucogenys	ENSNLEG00000016575	1 retrocopy	retro_nleu_1938,
Pan troglodytes	ENSPTRG00000002623	2 retrocopies	retro_ptro_1036, retro_ptro_2950,
Rattus norvegicus	ENSRNOG00000006554	1 retrocopy	retro_rnor_2124,
Ictidomys tridecemlineatus	ENSSTOG00000002142	1 retrocopy	retro_itri_429 ,