RetrogeneDB ID: retro_cfam_2070

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:43817681..43818680(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF2S2
• Ensembl ID: ENSCAFG00000007498
• Aliases: None
• Description: eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa [Source:HGNC Symbol;Acc:3266]

Sequence

>retro_cfam_2070
ATGTCCGGGGACGAGATGATTTTTGATCCAACTATGAGCAAGAAGAAAAAGAAGAAGAAGAAGCCTTTTATGTTAGATGA
GGAAGGGGATGCCCAGACGGAAGAAACCCAGCCCTCAGAAACAAAAGAAGTAGAACCAGAGCCAACTGAGGACAAAGATG
TAGAAGCTGATGAAGAGGACAGTAGGAAAAAGGATGCTTCTGATGATTTAGATGACTTGAACTTCTTTAATCAGAAGAAA
AAGAAGAAAAAAACAAAAAAGATATTTGATATTGATGAAGCTGAAGAAGGTGTAAAGTATCTTAAGATCGAAAGTGATAT
CCAAGAACCAGCTGAACCAGAGGATGACCTTGACATTATGCTTGGCAATAAAAAGAAGAAAAAGAAGAACGTTAAGTTCC
CAGATGAGGATGAAATACTAGAGAAAGATGAAGCTTTAGAAGATGAAGACAGCAAAAAAGATGATGGTATCTCATTCAGT
AACCAGACAGATCCTGCTTGGGCAGGCTCCGAAAGAGACTACACGTATGAGGAGCTACTGAATCGAGTGTTCAACATTAT
GAGGGAAAAGAATCCAGATATGGTTGCTGGAGAAAAAAGGAAATTTGTCATGAAACCTCCACAGGTTGTCCGAGTAGGAA
CAAAGAAAAGTTCTTTTGTCAACTTTACAGATATCTTTAAACTATTACATCGTCAGCCCAAACATCATCTTGCATTTTTA
TTGGCTGAATTGGGTACAAGTGGTTCTATAGATGGTAATAATCAACTTGTAATCAAAGGAAGATTCCAACAGAAACAGAT
AGAAAATGTTTTGAAAAGATATATCAAGGAATACGTTACCTGTCGTACGTGCCGATCACCGGACACAATCCTGTAAAAGG
ACACCCGACTCTATTTCTTACAGTGCGAAACTTGTCATTCTCCATGCTCTGTTGCCAGCATCAAAACCGGCTTCCAGGCT
GTCACAGGCAAGCGAGCACAGCTCCGTGCCAAAGCTAAC

Alignment

ORF - retro_cfam_2070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.59 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSFKQMIFDPTMSKKKKKKKKPFMLDEEGDAQTEETQPSETKEVEPEPTEDKDVEADEEDSRKKDASDDL
          .S...MIFDPTMS........PFMLDEEGDAQTEETQPSETKEVEPEPTEDKDVEADEEDSRKKDASDDL
Retrocopy MSGDEMIFDPTMSXXXXXXXXPFMLDEEGDAQTEETQPSETKEVEPEPTEDKDVEADEEDSRKKDASDDL

Parental  DDLNFFNQKKKKKKTKKIFDIDEAEEGVKDLKIESDIQEPAEPEDDLDIMLGNKKKKKKNVKFPDEDEIL
          DDLNFFN..........IFDIDEAEEGVK.LKIESDIQEPAEPEDDLDIMLGN.......VKFPDEDEIL
Retrocopy DDLNFFNXXXXXXXXXXIFDIDEAEEGVKYLKIESDIQEPAEPEDDLDIMLGNXXXXXXXVKFPDEDEIL

Parental  EKDEALEDEDSKKDDGISFSNQTGPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVV
          EKDEALEDEDSKKDDGISFSNQT.PAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVV
Retrocopy EKDEALEDEDSKKDDGISFSNQTDPAWAGSERDYTYEELLNRVFNIMREKNPDMVAGEKRKFVMKPPQVV

Parental  RVGTKKTSFVNFTDICKLLHRQPKHLLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLRRYIKEYVT
          RVGTKK.SFVNFTDI.KLLHRQPKH.LAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVL.RYIKEYVT
Retrocopy RVGTKKSSFVNFTDIFKLLHRQPKHHLAFLLAELGTSGSIDGNNQLVIKGRFQQKQIENVLKRYIKEYVT

Parental  CHTCRSPDTILQKDTRLYFLQCETCHSRCSVASIKTGFQAVTGKRAQLRAKAN
          C.TCRSPDTIL.KDTRLYFLQCETCHS.CSVASIKTGFQAVTGKRAQLRAKAN
Retrocopy CRTCRSPDTIL*KDTRLYFLQCETCHSPCSVASIKTGFQAVTGKRAQLRAKAN

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	1.93 RPM	41.79 RPM
SRP017611_brain	1.11 RPM	26.83 RPM
SRP017611_kidney	1.78 RPM	40.81 RPM
SRP017611_liver	0.87 RPM	15.74 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_cfam_2070 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
GR901448	43817744	43817964	100	220	0	220

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2070 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2070 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000007498	1 retrocopy	retro_cfam_2070 ,
Choloepus hoffmanni	ENSCHOG00000006521	1 retrocopy	retro_chof_271,
Callithrix jacchus	ENSCJAG00000018334	2 retrocopies	retro_cjac_4196, retro_cjac_697,
Cavia porcellus	ENSCPOG00000015439	1 retrocopy	retro_cpor_1143,
Echinops telfairi	ENSETEG00000001922	1 retrocopy	retro_etel_1101,
Myotis lucifugus	ENSMLUG00000005335	1 retrocopy	retro_mluc_604,
Monodelphis domestica	ENSMODG00000002805	5 retrocopies	retro_mdom_1981, retro_mdom_365, retro_mdom_368, retro_mdom_370, retro_mdom_837,
Mus musculus	ENSMUSG00000074656	1 retrocopy	retro_mmus_3200,
Otolemur garnettii	ENSOGAG00000001417	1 retrocopy	retro_ogar_196,
Pongo abelii	ENSPPYG00000010933	2 retrocopies	retro_pabe_1955, retro_pabe_2421,
Rattus norvegicus	ENSRNOG00000017447	1 retrocopy	retro_rnor_2395,
Tupaia belangeri	ENSTBEG00000009970	2 retrocopies	retro_tbel_1505, retro_tbel_2508,