RetrogeneDB ID: retro_itri_243

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:16715967..16716951(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPBP1L1
• Ensembl ID: ENSSTOG00000013491
• Aliases: None
• Description: GC-rich promoter binding protein 1-like 1 [Source:HGNC Symbol;Acc:28843]

Sequence

>retro_itri_243
GTGAGCCATTGTTGACACAATTCCTCTGATGAAAAAAGCCTTTTTAACAATGGGCCCCCTCGAACTACAGGAGATTCCTG
GCATCAGCCCTCCCTCTTCCGCCATGATTCTGTGGACTCTGGTGTCTCTAAGGGAACATATGCTGGAATCACAGGGAACC
TATCTGGTTGGCATAGTTCTTCCTGAGGTCATGATGGCATGAACCAGCGTAGAGGAGGTGGCACAGGGAACCATCAACAC
TGGAATGGCAGTTTTCATTCCGGAAAGGCTGTGCCTTTCAAGAAAAGCCACCTACAGAGATTAGGGAAGAAAAGAAAGAA
GACAAAGTAGAAAAGTTGCAGTTTGAAGAGGAAGACTTTCCTTCTTTGAATCCAGAAGCTGGCAAACAGAATCAGCCATG
CAGATCTATTGAGACCCCTTCTGGAGTGTGGGAAAACCCACCTAGTGCCAATCAACCCTCCAAGATTCTAGTTATCAAAA
AAGTTTCCAAAGAGGATCCTGCTGCTGTCTTCTCTGCTGCATTCACCTCACCAGGATCTCACATGCAAATGGGAACAAAT
CATCAACTATGGTTCCAAGTGTCTATAAGAACTTGGTTCCTAAGCCTGCACCACCTCTTTCCAAGCCCAATGCATGGAAA
TCTAGCAAAATGGAACACAAATCAGGATCTCTTTCCTCTGACCCGGAGTCATTTACCAATCCAATTTCTGTTACCAAACC
AGTGGTACTGGCTGGTGGTGCAGTTCTCAGCTCTCCCAAAGAGAGTCCCTCCAGCATTACCCCTCCAATTGAGATCAGCT
CCTCTCCTCTAAGTTGACCAGCCAAACCACTGACAGGAAGAGTGAATTCCTAAAGACTCTGAAGGATGACTGAAATGGAG
ACTTTGCAGAGAACAGAGACTGTGACAAGCTGGAGGATTTGGAGGACAACAGCACACCTGAACCAAAGGAAAATGGGGAG
GAAGGCTGTCTTCAGAATGGTCTC

Alignment

ORF - retro_itri_243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.09 %
• Parental protein coverage: 71.71 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  VSRRRHNSSD--GFFNNGPLRTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSSRGHDGINQR
          VS...HNSSD....FNNGP.RTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSS.GHDG.NQR
Retrocopy VSHC*HNSSDEKSLFNNGPPRTTGDSWHQPSLFRHDSVDSGVSKGTYAGITGNLSGWHSSS*GHDGMNQR

Parental  SGGGTGNHRHWNGSFHS-RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRPIGT
          .GGGTGNH.HWNGSFHS.RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCR.I.T
Retrocopy RGGGTGNHQHWNGSFHS<RKGCAFQEKPPTEIREEKKEDKVEKLQFEEEDFPSLNPEAGKQNQPCRSIET

Parental  PSGVWENPPSAKQPSKMLVIKKVSKEDPAAAFSAAFTSPGSH-HANGNKSSTMVPSVYKNLVPKPAPPPS
          PSGVWENPPSA.QPSK.LVIKKVSKEDPAA.FSAAFTSPGSH.HANGNKSSTMVPSVYKNLVPKPAPP.S
Retrocopy PSGVWENPPSANQPSKILVIKKVSKEDPAAVFSAAFTSPGSH<HANGNKSSTMVPSVYKNLVPKPAPPLS

Parental  KPNAWKSSRMEHKSGSLSSSRESSFTNPISVTKPVVLAGGTVLSSP-KESPSSITPPIEISSSRL-TKLT
          KPNAWKSS.MEHKSGSLSS..ES.FTNPISVTKPVVLAGG.VLSSP.K..P.....P....S..L..KLT
Retrocopy KPNAWKSSKMEHKSGSLSSDPES-FTNPISVTKPVVLAGGAVLSSP>KRVPPAL--PLQLRSAPL>SKLT

Parental  RRTTDRKSEFLKTLKDDRNGDFAENRDCDKLEDLLQLEDNSTPEPKENGEEGCLQNGL
          ..TTDRKSEFLKTLKDD.NGDFAENRDCDKLEDL...EDNSTPEPKENGEEGCLQNGL
Retrocopy SQTTDRKSEFLKTLKDD*NGDFAENRDCDKLEDL---EDNSTPEPKENGEEGCLQNGL

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_243 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_243 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
Choloepus hoffmanni	ENSCHOG00000010454	1 retrocopy	retro_chof_53,
Microcebus murinus	ENSMICG00000008449	1 retrocopy	retro_mmur_164,
Myotis lucifugus	ENSMLUG00000012432	2 retrocopies	retro_mluc_211, retro_mluc_834,
Mus musculus	ENSMUSG00000034042	2 retrocopies	retro_mmus_1391, retro_mmus_405,
Oryctolagus cuniculus	ENSOCUG00000017939	1 retrocopy	retro_ocun_427,
Otolemur garnettii	ENSOGAG00000004134	1 retrocopy	retro_ogar_1859,
Ochotona princeps	ENSOPRG00000001584	1 retrocopy	retro_opri_928,
Rattus norvegicus	ENSRNOG00000037595	1 retrocopy	retro_rnor_390,
Ictidomys tridecemlineatus	ENSSTOG00000003057	1 retrocopy	retro_itri_1678,
Ictidomys tridecemlineatus	ENSSTOG00000013491	1 retrocopy	retro_itri_243 ,