RetrogeneDB ID: retro_itri_698

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393312.1:3932202..3933578(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000024353
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SF1
• Ensembl ID: ENSSTOG00000009790
• Aliases: None
• Description: splicing factor 1 [Source:HGNC Symbol;Acc:12950]

Sequence

>retro_itri_698
AGGTCCCCTTCCCCTGAGCCCATCTACAATAGTGAGGGGAAGCAACTTAACACCAGAGAGTTCCGTACCCGCAAAAAGCT
GGAAGAGGAGCGGCACAACCTCATCACAGAGATGGTTGCCCTCAACCCTGATTTCAAGCCACCTGCAGATTATAAACCTC
CAGCAACACGTGTGAGTGATAAAGTAATGATCCCTCAAGATGAGTATCCAGAAATCAACTTTGTTGGGCTACTAATTGGG
CCCAGAGGGAACACCGTGAAGAATATTGAGAAGGAGTGCAACGCCAAGATCATGATCTGGGGGAAAGGGTCTGTGAAAGA
AGGGATGGTTGGGCGCAAAGATGGCCAGATGTTGCCAGGGGAAGATGAACCACTTCATGCCCTAGTCACTGCCAATACAA
TGGAGAATGTTAAAAAGGCAGTAGAGCAGATCAGAAACATCCTGAAGCAAGGTATTGAGACCCCAGAGGACCAGAATGAT
CTACGGAAGATGCAGCTTCGAGAATTGGCTCGCTTGAATGGTACCCTTCGGGAAGATGATAACAGAATCTTAAGACCCTG
GCAGAGCTCAGAGACCCGCAGCATTACCAATACTACAGTGTGTACCAAGTGTGGAGGAGCTGGCCACATTGCTTCAGATT
GCAAGTTTCAAAGGCCTGGTGACCCCCAGTCAGCTCAGGATAAAGCACGGATGGATAAAGAATATTTGTCCTTGATGGCT
GAACTTGGGGAAGCCCCTGTCCCAGCATCTGTGGGCTCCACCTCTTGGCCTGCGACCACACCCTTGGCTAGTGCACCTCG
GCCTGCTGCTCCTGCCAACAACCCACCTCCACCGTCTCTCATGTCCACCACCCAGAGCCGCCCACCCTGGATGAATTCTG
GCCCTTCAGAGAGTCGGCCTTATCATGGCATGCATGGAGGTGGTCCTGGCGGGCCTGGAGGTGGCCCCCACAGCTTCCCA
CACCCAGCCTGACAGGGGGGCATGGTGGACATCCCATGCAGCACAACCCAAATGGACCCCCACCCCCTTGGATGCAGCCA
CCACCACCACGGATGAACCAGGGCCCCCACCCACCTGGGCACCGTGGCCCTCCTCCAATGGATCAGTACCTGGGAAGTAC
GCCTGTGGGCTCTGGGGTCTATCGCCTGCATCAAGGAAAAGGTATGATGCCGCCTCCGCCTATGGGCATGATGCCGCCAC
CGCCGCCGCCTCCCAGTGGGCACCCCCCGCCCCCTCCCTCTGGTCCTCTTCCCCCATGGCAGCAGCAGCCTCCGCAGCAG
CCTCCGCCACCCCCTCCGCCCAGCAGCAGTATGGCTTCCAGTACCCCCTTGCCATGGCAGCAAAGATCCCTCCCCGCAGC
GGCGATGGCCGGATCC

Alignment

ORF - retro_itri_698 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.04 %
• Parental protein coverage: 71.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSPSPEPIYNSEGKRLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPATRVSDKVMIPQDEYP
          RSPSPEPIYNSEGK.LNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPATRVSDKVMIPQDEYP
Retrocopy RSPSPEPIYNSEGKQLNTREFRTRKKLEEERHNLITEMVALNPDFKPPADYKPPATRVSDKVMIPQDEYP

Parental  EINFVGLLIGPRGNTLKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGEDEPLHALVTANTMENVKKA
          EINFVGLLIGPRGNT.KNIEKECNAKIMI.GKGSVKEG.VGRKDGQMLPGEDEPLHALVTANTMENVKKA
Retrocopy EINFVGLLIGPRGNTVKNIEKECNAKIMIWGKGSVKEGMVGRKDGQMLPGEDEPLHALVTANTMENVKKA

Parental  VEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAGHI
          VEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAGHI
Retrocopy VEQIRNILKQGIETPEDQNDLRKMQLRELARLNGTLREDDNRILRPWQSSETRSITNTTVCTKCGGAGHI

Parental  ASDCKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSGPATTPLASAPRPAAPANNPPPPSL
          ASDCKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTS.PATTPLASAPRPAAPANNPPPPSL
Retrocopy ASDCKFQRPGDPQSAQDKARMDKEYLSLMAELGEAPVPASVGSTSWPATTPLASAPRPAAPANNPPPPSL

Parental  MSTTQSRPPWMNSGPSESRPYHGMHGGGPGGPGGGPHSFPHPLPSLTGGHGGHPMQHNPNGPPP-PWMQP
          MSTTQSRPPWMNSGPSESRPYHGMHGGGPGGPGGGPHSFPH..P...GG....P.......P.P.PWMQP
Retrocopy MSTTQSRPPWMNSGPSESRPYHGMHGGGPGGPGGGPHSFPH--PA*QGGMVDIPCSTTQMDPHP<PWMQP

Parental  PPPPMNQGPHPPGHHGPPPMDQYLGSTPVGSGVYRLHQGKGMMPPPPMGMMPPPPPPPSGQPPPPPSGPL
          PPP.MNQGPHPPGH.GPPPMDQYLGSTPVGSGVYRLHQGKGMMPPPPMGMMPPPPPPPSG.PPPPPSGPL
Retrocopy PPPRMNQGPHPPGHRGPPPMDQYLGSTPVGSGVYRLHQGKGMMPPPPMGMMPPPPPPPSGHPPPPPSGPL

Parental  PPWQQQQQQPPPPP-PPSSSMASSTPLPWQQNTTTTTTSAGT
          PPW..........P.PPSSSMASSTPLPWQQ........AG.
Retrocopy PPWXXXXXXXXXXPPPPSSSMASSTPLPWQQRSLPAAAMAGS

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_698 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_698 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017828	1 retrocopy	retro_amel_1763,
Canis familiaris	ENSCAFG00000014239	1 retrocopy	retro_cfam_2148,
Callithrix jacchus	ENSCJAG00000002780	1 retrocopy	retro_cjac_1930,
Ictidomys tridecemlineatus	ENSSTOG00000009790	1 retrocopy	retro_itri_698 ,