RetrogeneDB ID: retro_cfam_1496

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:12786642..12788334(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000029213
• 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_1496
ATGTCTTACCCCGCTGATGATTACGAGTCCGAGGCTGCTTATGATCCCTATGCTTACCCAGGCGACTATGATATGCACAC
AGGAGACCCAAAGCAGAATCTGGCTTACGAACGTCAGTATGAACAGCAGACCTATCAGGTGATCCTCGAAGTGATCAAAA
ACTTCATCCAGTATTTTCACAAAACCGTCTCGGATTTGATTGACCAGAAGGTGTATGAGCTGCAGGCTAGTCGTGTATCC
AGCGATGTCATTGATCAGAAAGTATATGAGATCCAGGACATCTATGAGAACAGCTGGACCAAGTTGACTGAAAGGTTCTT
CAAGAATACACCTTGGCCTGAGGCTGAAGCCATAGCTCCACAGGTTGGCAACGATGCCGTCTTCCTGATTTTGTACAAAG
AATTATACTACAGGCACATATATGCCAAAGTCAGTGGGGGCCCCTCCTTGGAGCAGAGGTTTGAATCCTACTACAACTAC
TGCAATCTCTTCAACTACATTCTTAATGCTGATGGTCCTGCTCCCCTTGAACTACCTAACCAGTGGCTTTGGGATATCAT
TGATGAGTTCATCTATCAGTTTCAGTCATTCAGCCAGTACCGCTGTAAGACTGCCAAGAAGTCAGAGGAAGAGATTGACT
TCCTTCGCTCCAATCCCAAAATCTGGAATGTTCACAGTGTCCTCAATGTCCTCCACTCCCTGGTCGACAAATCCAACATT
AACCGGCAATTGGAGGTGTACACAAATGGTGGTGACCCCGAGAGTGTGGCTGGTGAGTATGGACGGCACTCCCTTTACAA
GATGCTTGGGTATTTCAGCCTGGTGAGGCTTCTGCGTCTGCACTCCCTTTTAGGGGATTACTACCAGGCCATCAAGGTGC
TGGAGAATATTGAACTGAATAAGAAGAGTATGTATTCTCGTGTGCCTGAGTGCCAGGTCACCACATACTACTATGTCGGT
TTTGCATGTTTGATGATGCGTCGCTACCAGGCTGCCATCCGGGTATTTGCCAATATCCTCCTCTACATCCAAAGGACCAA
GAGCATGTTCCAAAGGACTACATACAAGTATGAGATGATTAACAAGCAAAATGAGCAGATGCACGCGCTGCTGGCCATCG
CCCTCACCATGTACCCCATGCGAATCGATGAGAGCATTCACCTGCAGCTGCGGGAAAAATACGGGGATAAGATGCTACAC
ATGCAGAAGGGTGACCCACAGGTCTATGAGGAACTTTTCAGTTACTCGTGCCCCAAATTCCTGTCACCTGTGGTGCCCAA
CTATGATAATGTGCACCCCAACTACCACAAGGAGCCCTTCCTGCAGCAGCTGAAGGTGTTTTCTGATGAAGTGCAGCAGC
AGGCCCAGCTCTCCACCATCCGTAGCTTCCTCAAGCTGTACACTACCATGCCTGTGGCCAAGCTGGCCGGCTTCCTGGAC
CTCACAGAGCAGGAGTTCAGGATCCAGCTCCTTGTCTTCAAGCATAAGATGAAGAACCTAGTGTGGACCAGTGGCATCTC
TGCCCTTGACGGTGAATTTCAGTCGGCATCCGAAGTTGACTTCTACATTGATAAGGACATGATCCACATTGCAGACACCA
AGGTCGCCAGGCGCTATGGGGATTTCTTCATCCGGCAGATTCACAAATTTGAGGAGTTCAATCGAACTCTGAAGAAGATG
GGACAGAGACCC

Alignment

ORF - retro_cfam_1496 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.58 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSYPADDYESEAAYDPYAYPGDYDMHTGDPKQDLAYERQYEQQTYQVIPEVIKNFIQYFHKTVSDLIDQK
          MSYPADDYESEAAYDPYAYPGDYDMHTGDPKQ.LAYERQYEQQTYQVI.EVIKNFIQYFHKTVSDLIDQK
Retrocopy MSYPADDYESEAAYDPYAYPGDYDMHTGDPKQNLAYERQYEQQTYQVILEVIKNFIQYFHKTVSDLIDQK

Parental  VYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYRHI
          VYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYRHI
Retrocopy VYELQASRVSSDVIDQKVYEIQDIYENSWTKLTERFFKNTPWPEAEAIAPQVGNDAVFLILYKELYYRHI

Parental  YAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKSEE
          YAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKSEE
Retrocopy YAKVSGGPSLEQRFESYYNYCNLFNYILNADGPAPLELPNQWLWDIIDEFIYQFQSFSQYRCKTAKKSEE

Parental  EIDFLRSNPKIWNVHSVLNVLHSLVDKSNINRQLEVYTSGGDPESVAGEYGRHSLYKMLGYFSLVGLLRL
          EIDFLRSNPKIWNVHSVLNVLHSLVDKSNINRQLEVYT.GGDPESVAGEYGRHSLYKMLGYFSLV.LLRL
Retrocopy EIDFLRSNPKIWNVHSVLNVLHSLVDKSNINRQLEVYTNGGDPESVAGEYGRHSLYKMLGYFSLVRLLRL

Parental  HSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFAYLMMRRYQDAIRVFANILLYIQRTKSMF
          HSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFA.LMMRRYQ.AIRVFANILLYIQRTKSMF
Retrocopy HSLLGDYYQAIKVLENIELNKKSMYSRVPECQVTTYYYVGFACLMMRRYQAAIRVFANILLYIQRTKSMF

Parental  QRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLRMQKGDPQVYEELFSYSCPKF
          QRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKML.MQKGDPQVYEELFSYSCPKF
Retrocopy QRTTYKYEMINKQNEQMHALLAIALTMYPMRIDESIHLQLREKYGDKMLHMQKGDPQVYEELFSYSCPKF

Parental  LSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEFRIQL
          LSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEFRIQL
Retrocopy LSPVVPNYDNVHPNYHKEPFLQQLKVFSDEVQQQAQLSTIRSFLKLYTTMPVAKLAGFLDLTEQEFRIQL

Parental  LVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGDFFIRQIHKFEELNRTLKKM
          LVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGDFFIRQIHKFEE.NRTLKKM
Retrocopy LVFKHKMKNLVWTSGISALDGEFQSASEVDFYIDKDMIHIADTKVARRYGDFFIRQIHKFEEFNRTLKKM

Parental  GQRP
          GQRP
Retrocopy GQRP

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	0.08 RPM	10.00 RPM
SRP017611_kidney	0.33 RPM	105.92 RPM
SRP017611_liver	0.29 RPM	24.22 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1496 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1496 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,