RetrogeneDB ID: retro_cfam_1503

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 32:27248998..27251134(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EEF2
• Ensembl ID: ENSCAFG00000019158
• Aliases: None
• Description: eukaryotic translation elongation factor 2 [Source:HGNC Symbol;Acc:3214]

Sequence

>retro_cfam_1503
GCCACTGCGGGGCGCATCAAGCCAGTGCTGATGAGGAACAAGATGGACCGGGCTCTGCCGGAGCTGCAGTTGGAGCCTGA
GGAGCTCTACCAGACCTTCCAGCGCCCTGTGGAGAACGTCAACGTCATCATTTCTACCTACGGGGAGGGCGAGAGCAGTC
CCATGGGCAACATCAGGATCGACCCCGTACTTGGGACCGTTGGTTTTGGGTCCGGACTCCACGGTGGGCCTTTACCTTGA
AGCAGTTTGCAGAGATGTATGTGGCCAAATTTGCTACCAAGGGCGAGGGCCAGCTGGGGCCTGCTGAGTGGACCAAGAAA
GTGGAGGACATGATGAAGAATCTGTGGGGTGACTGGTATTTTGATCCAGCCAACGGCAAATTCAGCAAGTCAGCCACCAG
CCCTGACGGCAAGAAGCTACGGCGGACGTTTTGCCAGCTCATCTTGGACCCTATTTTCAAGGCGTTTGACGCCATCATGA
ATTTCAAGAAAGAGGAGACAGCAAAGCTGATTGAAAAGCTGGACATCAAGCTGGACAGTGGAGGCAAAGATAAGGAAGGC
AAACCACTGCTGAAGGCTGTGATGCGCCGCTGGCTACCTGCCGGGGATGCTTTGCTGCAGATGATCACCATCCATCTGCC
TTCCCCTGTGACAGCCCAGAAATACCGCTGTGAGCTCTTGTATGAGGGCCCCCCAGACAACGAGGCAGCCATGGGCATTA
AAAGCTGTGACCCCAAAGGCCCTCTCATGATGTACATTCCTAAAATGGTGCCAACCTCTGACAAAGGTCAGTTCTATGCT
TTTGGTCGTGTATTCTCAGAGCTGGTGTCCACTGGCCTGAAAGTCAGGATCATGGTGCCCAACTACACCCCTGGGAAGAA
GGAGGACCTGTACCTGAAGCCCATCCAGAGAACAATCCTGATGATGGGCCGTTATGTTGAGCCTATTGAAGATGTGCTTT
GTGGGAACATTGTGGATCTGGTGGGAGTGGACCAGTTCCTGGTAAAGACTGGCACCATCACCATCTTTGAGCATGCCCAC
AACATGAAGGTGATGAAGTTCAGCGTGAGCCCCATTGTCCGGGTTGCTGTGGAGGCCAAGGATCCAGCTGACCTTCCCAA
GCTAGTGGAGGGTCTGAAACGGCTGGCCAAGTCAGACCCCATGGTGCAGTGCATCATTGAGGAGTCAGGGGAGCACATCA
TCGAGGGGGCTGGGGAGCTGCACCTGGAGATCTGTCTGAAGGACCTGGAGAAGGACCATGCGTGCATTCCCATCAAGAAA
TCTGACCCTGTAGTCCCCTACCATGAGACCGTCAGTGAGGAGTAGAATGTGCTCTGCTTGTCCAAGTCCCCCAACAAGCA
CAACTGGGTGTACATGAGGCACGGCCCTTCCCTGACGGCCTGGCTGAGGACATTGACAAGGGTGAGGTGTCAGCCCACCA
GGAGCTCAAGCAGCAGGCCCGCTATCTGGCTGAGAAGTATGAGTGGGATGTGGCTGAGGCCCGCAAGATCTGGTGCTTCG
GGCCTGACGGCACTGGCACCAACATCCTCACTGATATCACTAAGGGTGTGCAGTACCTCAATGAGATCAAGAATAGTGTG
GTAGCTGGCTTCCAGTGGGCCACCAAAGAGGGTGCTCTGTGTGAGGAAAACATAAGTGGTGTGCGCTTCCATGAGCACGA
TGTGACCCTGCACGTGGACGCCATCCACCGTGGGGGTGGCCAGATTATCCCCATTGCCCGGCACTGCCTCTACACCAGTG
TACTGACTGCCCAGCCCTGGCTTATGGAGCCTATCTACCTTGTGGAGATTCAGTGTCCAGAACAAGTGGTTGGTGGCATC
TATGATGTCCTGAATAGGAAGCTGGGTCACGTCTTTGAGGAGTCCCAGGTGGCAGGCACTCCCATGTTTGTTGTGAAGGC
CTACCTGCCTGTGAATGAGTCCTTTGGCTTCACTGCTGACCTGAGGTCCAACACCAGTGGCCAAGCCTTCCCCTAATGTG
TATTTGACCACTGGCAGATCCTGCCCCGGATCCCTTTGACAACACCAGCCGCCCCAGCCAGGTGGTGGCTGAAGCACCCA
AGCATAAAGGCTTGAAGGAAGGCATCCCTGCCCTGGACAACTTCCTGGACAAATTG

Alignment

ORF - retro_cfam_1503 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.39 %
• Parental protein coverage: 83.1 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AIAERIKPVLMMNKMDRALLELQLEPEELYQTFQRIVENVNVIISTYGEGESGPMGNIMIDPVLGTVGFG
          A.A.RIKPVLM.NKMDRAL.ELQLEPEELYQTFQR.VENVNVIISTYGEGES.PMGNI.IDPVLGTVGFG
Retrocopy ATAGRIKPVLMRNKMDRALPELQLEPEELYQTFQRPVENVNVIISTYGEGESSPMGNIRIDPVLGTVGFG

Parental  SGLHG-WAFTLKQFAEMYVAKFAAKGEGQLGPAERAKKVEDMMKKLWGDRYFDPANGKFSKSATSPDGKK
          SGLHG.WAFTLKQFAEMYVAKFA.KGEGQLGPAE..KKVEDMMK.LWGD.YFDPANGKFSKSATSPDGKK
Retrocopy SGLHG<WAFTLKQFAEMYVAKFATKGEGQLGPAEWTKKVEDMMKNLWGDWYFDPANGKFSKSATSPDGKK

Parental  LPRTFCQLILDPIFKVFDAIMNFKKEETAKLIEKLDIKLDSEDKDKEGKPLLKAVMRRWLPAGDALLQMI
          L.RTFCQLILDPIFK.FDAIMNFKKEETAKLIEKLDIKLDS..KDKEGKPLLKAVMRRWLPAGDALLQMI
Retrocopy LRRTFCQLILDPIFKAFDAIMNFKKEETAKLIEKLDIKLDSGGKDKEGKPLLKAVMRRWLPAGDALLQMI

Parental  TIHLPSPVTAQKYRCELLYEGPPDDEAAMGIKSCDPKGPLMMYISKMVPTSDKGRFYAFGRVFSGLVSTG
          TIHLPSPVTAQKYRCELLYEGPPD.EAAMGIKSCDPKGPLMMYI.KMVPTSDKG.FYAFGRVFS.LVSTG
Retrocopy TIHLPSPVTAQKYRCELLYEGPPDNEAAMGIKSCDPKGPLMMYIPKMVPTSDKGQFYAFGRVFSELVSTG

Parental  LKVRIMGPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVPCGNIVGLVGVDQFLVKTGTITTFEHAHNM
          LKVRIM.PNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDV.CGNIV.LVGVDQFLVKTGTIT.FEHAHNM
Retrocopy LKVRIMVPNYTPGKKEDLYLKPIQRTILMMGRYVEPIEDVLCGNIVDLVGVDQFLVKTGTITIFEHAHNM

Parental  RVMKFSVSPVVRVAVEAKNPADLPKLVEGLKRLAKSDPMVQCIIEESGEHIIAGAGELHLEICLKDLEED
          .VMKFSVSP.VRVAVEAK.PADLPKLVEGLKRLAKSDPMVQ.................HLEICLKDLE.D
Retrocopy KVMKFSVSPIVRVAVEAKDPADLPKLVEGLKRLAKSDPMVQXXXXXXXXXXXXXXXXXHLEICLKDLEKD

Parental  HACIPIKKSDPVVSYRETVSEESNVLCLSKSPNKHNRLYMK-ARPFPDGLAEDIDKGEVSARQELKQRAR
          HACIPIKKSDPVV.Y.ETVSEE.NVLCLSKSPNKHN..YM..ARPFPDGLAEDIDKGEVSA.QELKQ.AR
Retrocopy HACIPIKKSDPVVPYHETVSEE*NVLCLSKSPNKHNWVYMR<ARPFPDGLAEDIDKGEVSAHQELKQQAR

Parental  YLAEKYEWDVAEARKIWCFGPDGTGPNVLTDITKGVQYLNEIKDSVVAGFQWATKEGALCEENMRGVRFD
          YLAEKYEWDVAEARKIWCFGPDGTG.N.LTDITKGVQYLNEIK.SVVAGFQWATKEGALCEEN..GVRF.
Retrocopy YLAEKYEWDVAEARKIWCFGPDGTGTNILTDITKGVQYLNEIKNSVVAGFQWATKEGALCEENISGVRFH

Parental  VHDVTLHADAIHRGGGQIIPTARRCLYASVLTAQPRLMEPIYLVEIQCPEQVVGGIYGVLNRKRGHVFEE
          .HDVTLH.DAIHRGGGQIIP.AR.CLY.SVLTAQP.LMEPIYLVEIQCPEQVVGGIY.VLNRK.GHVFEE
Retrocopy EHDVTLHVDAIHRGGGQIIPIARHCLYTSVLTAQPWLMEPIYLVEIQCPEQVVGGIYDVLNRKLGHVFEE

Parental  SQVAGTPMFVVKAYLPVNESFGFTADLRSNTGGQAFPQCVFDHWQILP-GDPFDNTSRPSQVVAETRKRK
          SQVAGTPMFVVKAYLPVNESFGFTADLRSNT.GQAFP.CVFDHWQILP..DPFDNTSRPSQVVAE..K.K
Retrocopy SQVAGTPMFVVKAYLPVNESFGFTADLRSNTSGQAFP*CVFDHWQILP<PDPFDNTSRPSQVVAEAPKHK

Parental  GLKEGIPALDNFLDKL
          GLKEGIPALDNFLDKL
Retrocopy GLKEGIPALDNFLDKL

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	0.25 RPM	1534.85 RPM
SRP017611_brain	0.16 RPM	779.79 RPM
SRP017611_kidney	0.13 RPM	1623.85 RPM
SRP017611_liver	0.94 RPM	1151.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1503 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1503 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1503 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004258	2 retrocopies	retro_btau_1809, retro_btau_539,
Canis familiaris	ENSCAFG00000019158	1 retrocopy	retro_cfam_1503 ,
Latimeria chalumnae	ENSLACG00000011124	1 retrocopy	retro_lcha_83,
Macaca mulatta	ENSMMUG00000022767	1 retrocopy	retro_mmul_2026,
Monodelphis domestica	ENSMODG00000000750	1 retrocopy	retro_mdom_223,
Mus musculus	ENSMUSG00000034994	1 retrocopy	retro_mmus_2521,