RetrogeneDB ID: retro_cfam_2196

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:92607062..92608151(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GDI2
• Ensembl ID: ENSCAFG00000005223
• Aliases: GDI2, GDI-2
• Description: Canis lupus familiaris GDP dissociation inhibitor 2 (GDI2), mRNA. [Source:RefSeq mRNA;Acc:NM_001003184]

Sequence

>retro_cfam_2196
ATGGCCAATGGTCAGCTGGTGAAGATGCTGCTTTATACAGAGGTCACTCGTTATCTGGATTTCAAAGTGACTGAAGGGAG
CTTTGTCTACAAGGGAGGAAAAATCTACAAGGTTCCTTCCACTGAAGCAGAAGCCCTGGCATCTAGCTTAATGGGACTGT
TTGAAAAACGTCGCTTCAGAAAATTCCTAGTATATGTTGCCAACTTTGATGAAAAAGATCCCAGAACTTTTGAGGGCATC
GATCCTAAGAAGACTGCCATGCGGGAGGTGTACAAGAAATTTGACTTGGGACAAGATGTCATAGACTTTACTGGCCATGC
CCTGGCACTTTACAGGACCAATGACTATTTAGATCAGCCATGTTGTGAAACCATTAATAGGATTAAACTTTACAGGGAGT
CTCTGGCAAGATATGGCAAAAGCCCGTACCTCTACCCACTGTATGGCCTTGGGGAGCTGCCGCAGGGATTTGCAAGGCTA
AGTGCTATTTATGGTGGCACCTACATGCTCAATAAACCCATTGAAGAAATCATTGTGCAAAATGGCAAAGTGATTGGTGT
GAAATCTGAAGGAGCGGTTGCTCGCTGCAAGCAGCTCATCTGTGACCCCAGCTATGTCAAAGACCGGGTAGAGAAGGTGG
GCCAGTTCATCAGGGTTATCTGCATTCTCAGCCACCCCATCAAGAACACCAATGACGCCAACTCCTGCCAGATCATCATA
CCCCAGAACCAGGTCAATCGGAAGTCAGACATCTACGTGTGCATGATCTCTGCACACAATGTGGCCGCGCAAAGGAAGTA
CATTACCATAGTGAGCACGACGGTGGAGACCAAGGAACCCGAGAAGGAAATCAGACCAGCTTTGGGGCTTCTGGAACCAA
TTTAACAGAAATTCGTTAGCATCAGCGACCTCCTTGTACCCAAAAACCTGGGGACGGAAAGCCAGATCTTCATTTCCCGC
ACGTACGATGCTACAACTCACTTTGAGACCACCTGTGACGATATTAAAAACATCTACAGGAGGATGACGGGCTCCGAGTT
TGACTGTGAGGAAATGAAGCGCAAGAAGAACGACATCTACGGGGAAGAC

Alignment

ORF - retro_cfam_2196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.7 %
• Parental protein coverage: 84.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRFRKFLVYVANFD
          MANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRFRKFLVYVANFD
Retrocopy MANGQLVKMLLYTEVTRYLDFKVTEGSFVYKGGKIYKVPSTEAEALASSLMGLFEKRRFRKFLVYVANFD

Parental  EKDPRTFEGIDPKKTAMREVYKKFDLGQDVIDFTGHALALYRTDDYLDQPCCETINRIKLYSESLARYGK
          EKDPRTFEGIDPKKTAMREVYKKFDLGQDVIDFTGHALALYRT.DYLDQPCCETINRIKLY.ESLARYGK
Retrocopy EKDPRTFEGIDPKKTAMREVYKKFDLGQDVIDFTGHALALYRTNDYLDQPCCETINRIKLYRESLARYGK

Parental  SPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVIGVKSEGEVARCKQLICDPSYVKDRV
          SPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVIGVKSEG.VARCKQLICDPSYVKDRV
Retrocopy SPYLYPLYGLGELPQGFARLSAIYGGTYMLNKPIEEIIVQNGKVIGVKSEGAVARCKQLICDPSYVKDRV

Parental  EKVGQVIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMISSAHNVAAQGKYIAIVSTTVETKE
          EKVGQ.IRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMI.SAHNVAAQ.KYI.IVSTTVETKE
Retrocopy EKVGQFIRVICILSHPIKNTNDANSCQIIIPQNQVNRKSDIYVCMI-SAHNVAAQRKYITIVSTTVETKE

Parental  PEKEIRPALELLEPIEQKFVSISDLLVPKDLGTESQIFISRTYDATTHFETTCDDIKNIYKRMTGSEFDF
          PEKEIRPAL.LLEPI.QKFVSISDLLVPK.LGTESQIFISRTYDATTHFETTCDDIKNIY.RMTGSEFD.
Retrocopy PEKEIRPALGLLEPI*QKFVSISDLLVPKNLGTESQIFISRTYDATTHFETTCDDIKNIYRRMTGSEFDC

Parental  EEMKRKKNDIYGED
          EEMKRKKNDIYGED
Retrocopy EEMKRKKNDIYGED

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	0.71 RPM	92.36 RPM
SRP017611_brain	0.32 RPM	98.92 RPM
SRP017611_kidney	0.07 RPM	219.05 RPM
SRP017611_liver	0.44 RPM	166.49 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2196 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2196 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 10 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005316	1 retrocopy	retro_btau_1208,
Canis familiaris	ENSCAFG00000005223	2 retrocopies	retro_cfam_2196 , retro_cfam_886,
Canis familiaris	ENSCAFG00000017406	1 retrocopy	retro_cfam_1873,
Callithrix jacchus	ENSCJAG00000020512	2 retrocopies	retro_cjac_1168, retro_cjac_3115,
Cavia porcellus	ENSCPOG00000013449	1 retrocopy	retro_cpor_696,
Gorilla gorilla	ENSGGOG00000003623	1 retrocopy	retro_ggor_2590,
Mus musculus	ENSMUSG00000021218	2 retrocopies	retro_mmus_2971, retro_mmus_360,
Oryctolagus cuniculus	ENSOCUG00000005367	1 retrocopy	retro_ocun_69,
Ictidomys tridecemlineatus	ENSSTOG00000006449	1 retrocopy	retro_itri_757,
Tupaia belangeri	ENSTBEG00000011523	1 retrocopy	retro_tbel_644,