RetrogeneDB ID: retro_fcat_945

Retrocopy location

• Organism: Cat (Felis catus)
• Coordinates: B4:34145862..34146591(+)
• Located in intron of: ENSFCAG00000008078

Retrocopy information

• Ensembl ID: ENSFCAG00000023372
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSFCAG00000028446
• Aliases: None
• Description: None

Sequence

>retro_fcat_945
GAGAAGAAAAAGAAAGTTCCTACTGTGCCAGAAACTCTTAAGAAAAAGCGAAGGAATTTCGCAGAGTTGAAGATCAAGCA
TCTGAGAAAGAAGTTTGCCCAAAAGATGCTTCAAATGGCAAGGAGGAAGGTTATTTATGAAAAAGCTAAGCATTAACCAC
AAGGAATACAGGCAGATGTACAGAACTGAGATTCGAATGGCTAGAATGGCAAGAAAAATTGGCAACTTCTACGTACCTAC
GGAACCCAAATTGGCATTTGTCATTAGGATCAGAGGTATCAATGGTGTGAGCCCAAAGGTTCAAAAGGTGTTGCAGCTTC
TTCGCCTTCACCAGATCTTCAATGGCACCTTTGTTAAACTCAACAAAGCTTCAGTTAACATGCTAAGGATTGTGGAACCA
TATATAGCATGGAGGTACCCAAACCTGAAGTCAGTGAATGAACTGATCTACAAGTGTGGTTATGGCAAAATCAACAAGAA
GCAAATTGTCCTGACAGATAACACATCGATCACTCGATCTCTTGGTAAATACGGCATCATCTGCATGGAGGATCTGATTC
ATGAGATCTATACTGTTGGAAAACATTTCAAAGAAGCAAACAACTTTTTTGGCCCTTCAAATTATCTTCTCCACGAGGGG
GAATGAAAAAGAAGACCACCGATTTTGTAGAAGGTGGAGATGCTGACAACAGGGAAGACCAGATCAATAGGCTTATTAGA
AGAATGAAC

Alignment

ORF - retro_fcat_945 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.02 %
• Parental protein coverage: 96.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EKKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKH-YHKEYRQMYRTEIRMARM
          EKKKKVP.VPETLKKKRRNFAELKIK.LRKKFAQKML..ARRK.IYEKAKH..HKEYRQMYRTEIRMARM
Retrocopy EKKKKVPTVPETLKKKRRNFAELKIKHLRKKFAQKMLQMARRKVIYEKAKH>NHKEYRQMYRTEIRMARM

Parental  ARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFNGTFVKLNKASVNMLRIVEPYIAWGY
          ARK.GNFYVP.EPKLAFVIRIRGINGVSPKV.KVLQLLRL.QIFNGTFVKLNKASVNMLRIVEPYIAW.Y
Retrocopy ARKIGNFYVPTEPKLAFVIRIRGINGVSPKVQKVLQLLRLHQIFNGTFVKLNKASVNMLRIVEPYIAWRY

Parental  PNLKSVNELIYKRGYGKINKKRIALTDNTLIARSLGKYGIICMEDLIHEIYTVGKRFKEANNF-LWPFKL
          PNLKSVNELIYK.GYGKINKK.I.LTDNT.I.RSLGKYGIICMEDLIHEIYTVGK.FKEANNF..WPFKL
Retrocopy PNLKSVNELIYKCGYGKINKKQIVLTDNTSITRSLGKYGIICMEDLIHEIYTVGKHFKEANNF<FWPFKL

Parental  SSPRGGMKKKTTHFVEGGDAGNREDQINRLIRRMN
          SSPRGGMKKKTT.FVEGGDA.NREDQINRLIRRMN
Retrocopy SSPRGGMKKKTTDFVEGGDADNREDQINRLIRRMN

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
SRP017611_brain	0.69 RPM	224.84 RPM
SRP017611_kidney	2.68 RPM	1226.90 RPM
SRP017611_liver	1.01 RPM	467.84 RPM

ChIP-Seq

Felis catus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_fcat_945 retrocopy.

TSS

Felis catus was not studied using FANTOM5 data.

Lab

retro_fcat_945 was not experimentally validated.

Homology

Retrocopy orthology:

Felis catus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 72 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001821	5 retrocopies	retro_amel_1230, retro_amel_1632, retro_amel_760, retro_amel_933, retro_amel_937,
Canis familiaris	ENSCAFG00000008021	28 retrocopies	retro_cfam_1039, retro_cfam_1075, retro_cfam_1079, retro_cfam_1167, retro_cfam_1209, retro_cfam_1236, retro_cfam_1270, retro_cfam_1308, retro_cfam_1390, retro_cfam_1436, retro_cfam_1445, retro_cfam_1453, retro_cfam_1524, retro_cfam_1541, retro_cfam_1699, retro_cfam_1755, retro_cfam_1855, retro_cfam_1856, retro_cfam_2051, retro_cfam_2192, retro_cfam_338, retro_cfam_403, retro_cfam_563, retro_cfam_609, retro_cfam_737, retro_cfam_74, retro_cfam_922, retro_cfam_998,
Dasypus novemcinctus	ENSDNOG00000017654	15 retrocopies	retro_dnov_1561, retro_dnov_1692, retro_dnov_182, retro_dnov_1893, retro_dnov_209, retro_dnov_2158, retro_dnov_2568, retro_dnov_264, retro_dnov_2657, retro_dnov_279, retro_dnov_287, retro_dnov_365, retro_dnov_655, retro_dnov_77, retro_dnov_971,
Felis catus	ENSFCAG00000009707	1 retrocopy	retro_fcat_143,
Felis catus	ENSFCAG00000028446	6 retrocopies	retro_fcat_1643, retro_fcat_230, retro_fcat_255, retro_fcat_338, retro_fcat_342, retro_fcat_945 ,
Latimeria chalumnae	ENSLACG00000003571	1 retrocopy	retro_lcha_63,
Macropus eugenii	ENSMEUG00000016319	9 retrocopies	retro_meug_1002, retro_meug_1449, retro_meug_1942, retro_meug_1947, retro_meug_60, retro_meug_760, retro_meug_84, retro_meug_968, retro_meug_99,
Monodelphis domestica	ENSMODG00000007136	4 retrocopies	retro_mdom_1341, retro_mdom_1998, retro_mdom_371, retro_mdom_66,
Sus scrofa	ENSSSCG00000006182	3 retrocopies	retro_sscr_1138, retro_sscr_209, retro_sscr_796,