RetrogeneDB ID: retro_cfam_1096

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 23:3626667..3627791(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ESRP1
• Ensembl ID: ENSCAFG00000009305
• Aliases: ESRP1, RBM35A
• Description: epithelial splicing regulatory protein 1 [Source:HGNC Symbol;Acc:25966]

Sequence

>retro_cfam_1096
ATTGCTGGTGGAACATCTAATGAGGGAGCCCTTTTTTTCTCCAAGGAAAATGGAGGGGGGGTTTGCATGCCGGGCTCCTG
TTTACGGCCACGGCAGATGACGTGGTGGCCTTCTTCGGACAGCACTGCCCCATCACTGGGGGGAAGGAAGACATCCTCTT
TGTTACCTATCCAGATGGTAGGCCAACAGGGGGTGCCTTTGTCCTCTTTGCCTGTGAAGAATATACACAGAATGCATTGA
GGAAGCATAAGACTTGTTGGGTAAAAGATACATTGAACTCTTCAGGAGCACAGCAGCTAAAGTCCAGCAAGTGCTGAACC
GATTCTCTTTGGCCCCTCTTATTCCACTTCCAACCCCCCCCCCCCCACCGTTATTCCAATATTACCTAAGCAATTCGTGC
CCCCTACGAATGTTAAGAGACTGTATATGCCTTTGTGGCCTTCCCTATGTGGCCACCATTGAGGACATCCTGGACGTCCT
GGGGAGTTTTCTACGGGTATTTGAACGCATGGGGTGCACGTGGTATTGAATCACCAGGGCCGCCCATCAGGAGATGCCTT
TATCCAGATGAAGTTTGCGGACAGAGCATTTATGGCTGCACAGAAGTGTCATTAAAAAAACCATGAAGGACAGATATGTT
GAAGTCTTTCAGTGTTCAGCTGAGATGAACTTTGTATTAAAGGGGGGTGCTTTAAATCGAAATGGCTATCCCCACCGCCA
TGTAAGTTACCATGCCTGTTTCCTCCCTCCTCCACATTTCCAGCTCCTGCAGCAGTCATTCCTATGGAAGCTGCCATTTA
TCAGCCCTCCGTGCTTTTGAATCTTTGGGCGCTACAGCCCTCCACCGTGTACTCCCCAGCGGGCACCCAGCTATTCATGA
ACTACACTGCGTGCTATCCCAGCTCCCCAGGTTTGCCCACTAGTCTTGGCTACTTCCCTACAGCTGCTAATCTTAGCGGT
GTCCCTCCACAGCCTGGCACAGTGGTCAGAATGCAGGGTCTGGCCTACAATACTGGAGTTAAGGAAATTCTTAACTTCTT
CAAGGTTACCAGTATGCAGCCAGTGATGGACTTGTACACACAAATGACCAGGCCAGGACTCTACCCAAAGAATGGGTTTG
TATT

Alignment

ORF - retro_cfam_1096 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 71.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  IAGGTSNEVAQFLSKENQVIVRM-RGLPFTATADEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVL
          IAGGTSNE.A.F.SKEN...V.M..GL.FTATAD.VVAFFGQHCPITGGKE.ILFVTYPDGRPTG.AFVL
Retrocopy IAGGTSNEGALFFSKENGGGVCM<AGLLFTATADDVVAFFGQHCPITGGKEDILFVTYPDGRPTGGAFVL

Parental  FACEEYAQNALRKHK-DLLGKRYIELFRSTAAEVQQVLNRFSSAPLIPLPTPPIIP-VLP---QQFVPPT
          FACEEY.QNALRKHK.DLLGKRYIELFRSTAA.VQQVLNRFS.APLIPLP.....P.V.P....QFVPPT
Retrocopy FACEEYTQNALRKHK<DLLGKRYIELFRSTAAKVQQVLNRFSLAPLIPLPXXXXXP<VIPILPKQFVPPT

Parental  NV-RDCIRLRGLPYAATIEDILDFL-GEFSTDIRTHGVHMVLNHQGRPSGDAFIQMKSADRAFMAAQKCH
          NV.RDCI.L.GLPY.ATIEDILD.L.GEFST.I.THGVH.VLNHQGRPSGDAFIQMK.ADRAFMAAQKCH
Retrocopy NV>RDCICLCGLPYVATIEDILDVL<GEFSTGI*THGVHVVLNHQGRPSGDAFIQMKFADRAFMAAQKCH

Parental  -KKTMKDRYVEVFQCSAEEMNFVLMGGTLNRNG-LSPPPCKLPCLSPPSYTFPAPAAVIPTEAAIYQPSV
          .KKTMKDRYVEVFQCSA.EMNFVL.GG.LNRNG.LSPPPCKLPCL.PPS.TFPAPAAVIP.EAAIYQPSV
Retrocopy >KKTMKDRYVEVFQCSA-EMNFVLKGGALNRNG<LSPPPCKLPCLFPPSSTFPAPAAVIPMEAAIYQPSV

Parental  LLNPRALQPSTAYYPAGTQLFMNYTAYYPSSPGSPTSLGYFPTAASLSGVPPQPGTVVRMQGLAYNTGVK
          LLN..ALQPST.Y.PAGTQLFMNYTA.YPSSPG.PTSLGYFPTAA.LSGVPPQPGTVVRMQGLAYNTGVK
Retrocopy LLNLWALQPSTVYSPAGTQLFMNYTACYPSSPGLPTSLGYFPTAANLSGVPPQPGTVVRMQGLAYNTGVK

Parental  EILNFF-QGYQYAADDGLVHTNDQARTLPKEWVCI
          EILNFF.QGYQYAA.DGLVHTNDQARTLPKEWVCI
Retrocopy EILNFF<QGYQYAASDGLVHTNDQARTLPKEWVCI

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	0.00 RPM	0.04 RPM
SRP017611_brain	0.08 RPM	0.00 RPM
SRP017611_kidney	0.00 RPM	10.10 RPM
SRP017611_liver	0.00 RPM	0.44 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1096 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1096 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1096 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021838	1 retrocopy	retro_btau_847,
Canis familiaris	ENSCAFG00000000336	2 retrocopies	retro_cfam_200, retro_cfam_230,
Canis familiaris	ENSCAFG00000009305	1 retrocopy	retro_cfam_1096 ,