RetrogeneDB ID: retro_cfam_315

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:65806163..65807853(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000001066
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF3L
• Ensembl ID: ENSCAFG00000001443
• Aliases: EIF3L, EIF3EIP, EIF3S6IP
• Description: Canis lupus familiaris eukaryotic translation initiation factor 3, subunit L (EIF3L), mRNA. [Source:RefSeq mRNA;Acc:NM_001251940]

Sequence

>retro_cfam_315
ATGTCTTACCCCGCTGATGATTACGAGTCCGAGGCTGCTTATGATCCCTATGCTTACCCAGGCGACTACGATATGCACAC
AGGAGACCCAAAGCAGGATCTGGCTTACGAACGTCAGTATGAACAGCAGACCTATCAGGTGATCCCTGAAGTGATCAAAA
ACTTCATCCAGTATTTTCACAAAACCGTCTCGGATTTGATTGACCAGAAGGTGTATGAGCTGCAGGCTAGTCGTGTATCC
AGCGATGTCATTGATCAGAAAGTATATGAGATCCAGGACATCTATGAGAACAGCTGGACCAAGTTGACTGAAAGGTTCTT
CAAGAATACACCTTGGCCTGAGGCTGAAGCCATAGCTCCACAGGTTGGCAACGATGCCGTCTTCCTGATTTTGTACAAAG
AATTCTACTACAGGCACATATATGCCAAAGTCAGTGGGGGCCCCTCCTTGGAGCAGAGGTTTGAATCCTACTACAACTAC
TGCAATCTCTTCAACTACATTCTTAATGCTGATGGTCCTGCTCCCCTTGAACTACCTAACCAGTGGCTTTGGGATATCAT
TGATGAGTTCATCTATCAGTTTCAGTCATTTAGCCAGTACTGCTGTAAGACTGCCAAGAAGTCAGAGGAAGAGATTGACT
TCCTTTGCTCCAATCCCAAAATCTGGAATGTTCAGTGTCCTCAATGTCCTCCACTCCCTGGTCGAAAAATCCAACATTAA
CCGGCAATTGGAGGTGTACACAAGTGGTGGTGACCCCAAGAGTGTGGCTGGCGAGTATGGACGGCACTCCCTTTACAAGA
TGCTTGGGTATTTCAGCCTGGTGGGGCTTCTGCGTCTGCACTCCCTTTTAGGGGATTACTACCAGGCCATCAAGGTGCTG
GAGAATATTGAACTGAATAAGAAGAGTATGTATTCTCGTGTGCCTGAGTGTCAGGTCACCACATACTACTATGTCGGTTT
TGCATATTTGATGATGCATCGCTACCAGGATGCCATCCGGGTATTTGCCAATATCCTCCTCTACATCCAAAGGACCAAGA
GCATGTTCCAAAGGACTACATACAAGTATGAGATGATTAACAAGCAAAATGAGCAGATGCTCGCGCTGCTGGCCATCGCC
CTCACCATGTACCCCATGCGAATCGATGAGATCATTCACCTGCAGCTGCGGAAGAAATACGGGGATAAGATGCTATGCAT
GCAGAAGGGTGACCCACAGGTCTATGAGGAACTTTTCAGTTACTCGTGCCCCAAATTCCTGTCACCTGTGGTGCCCAACT
ATGATAATGTGCACCCCAACTACCACAAGGAGCCCTTCTTGCAGCAGCTGAAGGTGTTTTCTGATGAAGTGCAGCATCAG
GCCCAGCTCTCCACCATCCGTAGCTTCCTCAAGCTGTACACTACCATGCCTGTGGCCAAGCTGGCCGGCTTCCTGGACCT
CACAGAGCAGGAGTTCAGGATCCAGCTCCTTGTCTTCAAGCATAAGATGAAGAACCTAGTGTGGACCAGTGGCATCTCTG
CCCTTGACGGTGAATTTCAGTCGGCATCCGAAGTTGACTTCTACATTGATAAGGACATGATCCACATTGCAGACACCAAG
GTCGCCAGGCGCTATGGGGATTTCTTCATCCGGCAGATTCACAAATTTGAGGAGCTCAATCGAACTCTGAAGAAGATGGG
ACAGAGACCC

Alignment

ORF - retro_cfam_315 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.99 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSYPADDYESEAAYDPYAYPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFHKTVSDLIDQK
          MSYPADDYESEAAYDPYAYPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFHKTVSDLIDQK
Retrocopy MSYPADDYESEAAYDPYAYPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFHKTVSDLIDQK

Parental  VYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYRHI
          VYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKE.YYRHI
Retrocopy VYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKEFYYRHI

Parental  YAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKSEE
          YAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQY.CKTAKKSEE
Retrocopy YAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYCCKTAKKSEE

Parental  EIDFLRSN-PKIWNVHSVLNVLHSLVDKSNINRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLR
          EIDFL.SN.PK.....SVLNVLHSLV.KSNINRQLEVYTSGGDP.SVAGEYGRHSLYKMLGYFSLVGLLR
Retrocopy EIDFLCSN>PKS-GMFSVLNVLHSLVEKSNINRQLEVYTSGGDPKSVAGEYGRHSLYKMLGYFSLVGLLR

Parental  LHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSM
          LHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMM.RYQDAIRVFANILLYIQRTKSM
Retrocopy LHSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMHRYQDAIRVFANILLYIQRTKSM

Parental  FQRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPK
          FQRTTYKYEMINKQNEQM.ALLAIALTMYPMRIDE.IHLQLR.KYGDKML.MQKGDPQVYEELFSYSCPK
Retrocopy FQRTTYKYEMINKQNEQMLALLAIALTMYPMRIDEIIHLQLRKKYGDKMLCMQKGDPQVYEELFSYSCPK

Parental  FLSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEFRIQ
          FLSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQ.QAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEFRIQ
Retrocopy FLSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQHQAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEFRIQ

Parental  LLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGDFFIRQIHKFEELNRTLKK
          LLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGDFFIRQIHKFEELNRTLKK
Retrocopy LLVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGDFFIRQIHKFEELNRTLKK

Parental  MGQRP
          MGQRP
Retrocopy MGQRP

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	0.04 RPM	25.41 RPM
SRP017611_brain	0.00 RPM	10.00 RPM
SRP017611_kidney	0.13 RPM	105.92 RPM
SRP017611_liver	0.07 RPM	24.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_315 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_315 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_315 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001443	3 retrocopies	retro_cfam_1496, retro_cfam_1877, retro_cfam_315 ,
Monodelphis domestica	ENSMODG00000019068	3 retrocopies	retro_mdom_1247, retro_mdom_1585, retro_mdom_432,
Otolemur garnettii	ENSOGAG00000029444	1 retrocopy	retro_ogar_1635,
Pongo abelii	ENSPPYG00000011806	2 retrocopies	retro_pabe_1135, retro_pabe_1136,
Pteropus vampyrus	ENSPVAG00000010103	1 retrocopy	retro_pvam_648,