RetrogeneDB ID: retro_cpor_1484

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_9:47332011..47333883(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000005115
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SESTD1
• Ensembl ID: ENSCPOG00000025835
• Aliases: None
• Description: None

Sequence

>retro_cpor_1484
ATGGAAGCCTCTGTTATATTACCCATTCTGAAGAAGAAGCTGGCCTTCCTGTCCGGAGGAAAGGACAGACGAAGTGGCCT
CATTCTGACAATTCCATTATGCCTTGAACAAACAAATATGGATGAATTGAGTGTCACTTTGGACTATCTACTCAGCATTC
CAAGCGAAAAGTGTAAAGCTAGAGGATTTACTGTGATTGTAGATGGCAGAAAATCACAATGGAATGTGGTGAAAACAGTA
GTCTTAATGCTACAGAATGTTGTTCCAGCTGAAGTGTCCCTTGTTTGTGTAGTGAAGCCAGATGAGTTCTGGGATAAGAA
AGTAACACACTTTTGTTTTTGGAAAGAAAAGGATAGACTTGGCTTTGAGGTTATTTTAGTGTCTGCCAATAAATTGACTC
GTTACATTGAGCCATGCCAGTTAACAGAAGATTTTGGTGGGAGCCTCACCTATGATCACATGGATTGGTTAAATAAGAGG
CTGGTTTTTGAGAAGTTTACAAAGGAATCTACTTCATTATTAGATGAACTTGCTTTGATTAACAATGGTAGTGATAAAGG
AAATCAGCAAGAGAAAGAAAGGTCCGTGGATTTAAACTTTCTTCCATCAGTTGATCCTGAAACAGTTCTTCAGACAGGAC
ATGAATTGTTATCCGAATTACAGCAGCGTCGATTTAATGGCTCCGACGGAGGAGTCTCATGGTCTCCTATGGATGATGAA
CTGCTTGCCCAGCCACAGGTTATGAAATTATTAGATTCACTCCGAGAGCAGTATACTCGCTACCAGGAAGTCTGTAGGCA
GCGTAGCAAGCGCACACAGTTAGAAGAGATTCAACAGAAGGTGATGCAGGTCGTGAATTGGCTTGAAGGACCCGGATCTG
AACAGCTGAGAGCCCAGTGGGGGATTGGTGACTCCATCAGGGCTTCCCAGGCCCTGCAGCAGAAGCACGAAGAGATCGAG
AGCCAGCACAGTGAATGGTTTGCAGTATATGTGGAGCTTAATCAGCAAATTGCAGCACTCTTAAATGCCGGAGATGAGGA
AGATCTGGTGGAACTGAAGTCCCTGCAGCAGCAACTTAGTGACGTTTGCTATCGACAGGCCAGTCAGCTGGAATTTAGGC
AAAATCTCTTGCAAGCAGCTCTAGAATTTCATGGTGTTGCCCAAGATTTGTCTCAGCAGTTGGATGGCTTATTAGGGATG
TTGTGCGTAGATGTAGCACCAGCTGATGGAGCATCGATTCAGCAAACTTTAAAACTGCTTGAAGAGAAGCTGAAAAGTGT
TGATGTAGGATTGCAAGGATTGTGTGAAAAAGGTCAAGGTCTCCTGGATCAGATCTCCAATCAGGCATCCTGGGCCTATG
GAAAGGATGTAACCATTGAAAATAAAGAAAATGTGGATCATATACAAGGAGTGATGGAAGATATGCAACTTAGAAAACAA
AGATGTGAAGACATGGTAGATGTGCGAAGGTTAAAGATGCTTCAGATGGTGCAGCTATTTAAATGTGAAGAAGACGCTGC
CCAGGCTGTCAAATGGCTGAGTGAACTGCTGGATGCTCTCCTTAAGACCCACACGAGACTGGGCGATGATGCCCAGGAAA
CGAAAGTTCTCCTGGAAAAGCATCGAAAATTTGTTGATGTTGCACAGAGCACTTATGACTACGGGAGACAGTTGCTGCAG
GCCACGGTGGTGTTGTGCCAGTCTTTGCGCTGCACCTCTCGGTCCTCTGGGGACACGCTTCCTCGCCTGAACAGAGTGTG
GAAACAGTTTACAGTAGCATCTGAAGAAAGGGTGCATAGGCTGGAGATGGCTATTGCATTTCACTCAAATGCTGAAAAGA
TTTTGCAGGACTGTCCAGAAGAGCCTGAAACT

Alignment

ORF - retro_cpor_1484 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.68 %
• Parental protein coverage: 89.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEASVILPILKKKLAFLSGGKDRRSGLILTIPLCLEQTNMDELSVTLDYLLSIPSEKCKARGFTVIVDGR
          MEASVILPILKKKLAFLSGGKDRRSGLILTIPLCLEQTNMDELSVTLDYLLSIPSEKCKARGFTVIVDGR
Retrocopy MEASVILPILKKKLAFLSGGKDRRSGLILTIPLCLEQTNMDELSVTLDYLLSIPSEKCKARGFTVIVDGR

Parental  KSQWNVVKTVVLMLQNVVPAEVSLVCVVKPDEFWDKKVTHFCFWKEKDRLGFEVILVSANKLTRYIEPCQ
          KSQWNVVKTVVLMLQNVVPAEVSLVCVVKPDEFWDKKVTHFCFWKEKDRLGFEVILVSANKLTRYIEPCQ
Retrocopy KSQWNVVKTVVLMLQNVVPAEVSLVCVVKPDEFWDKKVTHFCFWKEKDRLGFEVILVSANKLTRYIEPCQ

Parental  LTEDFGGSLTYDHMDWLNKRLVFEKFTKESTSLLDELALINNGSDKGNQQEKERSVDLNFLPSVDPETVL
          LTEDFGGSLTYDHMDWLNKRLVFEKFTKESTSLLDELALINNGSDKGNQQEKERSVDLNFLPSVDPETVL
Retrocopy LTEDFGGSLTYDHMDWLNKRLVFEKFTKESTSLLDELALINNGSDKGNQQEKERSVDLNFLPSVDPETVL

Parental  QTGHELLSELQQRRFNGSDGGVSWSPMDDELLAQPQVMKLLDSLREQYTRYQEVCRQRSKRTQLEEIQQK
          QTGHELLSELQQRRFNGSDGGVSWSPMDDELLAQPQVMKLLDSLREQYTRYQEVCRQRSKRTQLEEIQQK
Retrocopy QTGHELLSELQQRRFNGSDGGVSWSPMDDELLAQPQVMKLLDSLREQYTRYQEVCRQRSKRTQLEEIQQK

Parental  VMQVVNWLEGPGSEQLRAQWGIGDSIRASQALQQKHEEIESQHSEWFAVYVELNQQIAALLNAGDEEDLV
          VMQVVNWLEGPGSEQLRAQWGIGDSIRASQALQQKHEEIESQHSEWFAVYVELNQQIAALLNAGDEEDLV
Retrocopy VMQVVNWLEGPGSEQLRAQWGIGDSIRASQALQQKHEEIESQHSEWFAVYVELNQQIAALLNAGDEEDLV

Parental  ELKSLQQQLSDVCYRQASQLEFRQNLLQAALEFHGVAQDLSQQLDGLLGMLCVDVAPADGASIQQTLKLL
          ELKSLQQQLSDVCYRQASQLEFRQNLLQAALEFHGVAQDLSQQLDGLLGMLCVDVAPADGASIQQTLKLL
Retrocopy ELKSLQQQLSDVCYRQASQLEFRQNLLQAALEFHGVAQDLSQQLDGLLGMLCVDVAPADGASIQQTLKLL

Parental  EEKLKSVDVGLQGLREKGQGLLDQISNQASWAYGKDVTIENKENVDHIQGVMEDMQLRKQRCEDMVDVRR
          EEKLKSVDVGLQGL.EKGQGLLDQISNQASWAYGKDVTIENKENVDHIQGVMEDMQLRKQRCEDMVDVRR
Retrocopy EEKLKSVDVGLQGLCEKGQGLLDQISNQASWAYGKDVTIENKENVDHIQGVMEDMQLRKQRCEDMVDVRR

Parental  LKMLQMVQLFKCEEDAAQAVEWLSELLDALLKTHTRLGDDAQETKVLLEKHRKFVDVAQSTYDYGRQLLQ
          LKMLQMVQLFKCEEDAAQAV.WLSELLDALLKTHTRLGDDAQETKVLLEKHRKFVDVAQSTYDYGRQLLQ
Retrocopy LKMLQMVQLFKCEEDAAQAVKWLSELLDALLKTHTRLGDDAQETKVLLEKHRKFVDVAQSTYDYGRQLLQ

Parental  ATVVLCQSLRCTSRSSGDTLPRLNRVWKQFTVASEERVHRLEMAIAFHSNAEKILQDCPEEPET
          ATVVLCQSLRCTSRSSGDTLPRLNRVWKQFTVASEERVHRLEMAIAFHSNAEKILQDCPEEPET
Retrocopy ATVVLCQSLRCTSRSSGDTLPRLNRVWKQFTVASEERVHRLEMAIAFHSNAEKILQDCPEEPET

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	0.29 RPM	10.35 RPM
SRP017611_kidney	1.57 RPM	25.33 RPM
SRP017611_liver	0.13 RPM	1.96 RPM
SRP040447_lung	0.40 RPM	34.20 RPM
SRP040447_skeletal_muscle	0.04 RPM	3.15 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1484 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1484 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000025835	1 retrocopy	retro_cpor_1484 ,